How isn't it the case?
Modern UI Applications are designed to complement, not replace, Desktop Applications. (No literature from MS I can find implies otherwise)
Microsoft is trying to, or at least wanting to
The Modern UI Components are tailored for casual users and usage on tablets and touch-screens as their primary usage scenario. This is why with every single Desktop Application that has a Modern-UI equivalent, the modern-UI equivalent has far fewer features. The goal is of shared code-bases a 'la the Threshold project. the two are considered complementary (for the obvious reason that no Modern UI app could be a Modern UI app and rival the capabilities of a Desktop application. In the same vein, no Desktop application could keep all it's options and capabilities while still remaining touch-friendly and accessible.). Bear in mind that the Modern UI and it's various libraries and technologies is catered almost entirely for the creation and distribution of Windows Store Applications. The idea being that general applications can be created via the Modern UI architecture and be run on tablets, smartphones, and other Windows-8-based devices, but still be able to run just as well on desktops equipped with Windows 8. Of course those mobile devices will not have a desktop (and they never did, not in the traditional sense) but Desktop computers have had a desktop and they need to remain compatible. Microsoft does not have a history of making clean breaks with old software and Windows 8 is no exception.
This is also not a case akin to WoW32, wherein Windows 3.1 applications were still runnable in Windows 95, but only for compatibility reasons and those applications were encouraged to be ported to the new API (Win32). For Desktop Applications Microsoft is not issuing a similar "Call to action" as they did with the Win32 API to move those Win32 Application to the Modern UI because the Modern UI is not something that can be used for all types of applications, particularly with the security limitations that a Modern UI Application must adhere to- in particular, Modern UI Application
cannot access the local file system nor can they use third-party libraries. The design purpose is effectively that Modern UI Applications won't actually have any particularly heavy logic and will just be the user-interface towards some back-end web service- since HTTP/Asynchronous XML is pretty much the only thing a Modern UI Application can actually do.
If not then the Modern UI has no logical reason to exist because the Desktop has worked just fine for many years.
The Desktop has worked fine for many years
on desktop computers. The goal is to have a single set of Windows Editions based on a single codebase and with similar capabilities. A Application written for Windows 7 cannot run on Windows Phone 7, and a App designed for Windows Phone 7 cannot run on Windows 7. The goal is to allow a developer to select their target(s) and develop in a way that makes that product most accessible with the least effort. If they want to target Phones and Tablets as well as desktops, they can create a Windows Store Application. If their application requires more fine-grained capabilities, more significant options, or references other libraries that cannot be abstracted to a web service effectively, than it can be made as a standard desktop application. And of course applications can do both, as Internet Explorer does.
I downloaded the source to the Firefox beta with Modern UI capabilities, and from what I can tell it is two separate apps- the modern UI version written in javascript, and the desktop version of course using C++. More interestingly, however, is that the touch/Modern UI Firefox application can only run on x86/x64 machines that can execute .exe files, so effectively Firefox's Modern UI can only ever be run on desktop systems (the js files rely on some C++ stub programs, for whatever reason). It seems that the push to create it was based on the mistaken impression that the Modern UI is going to replace the desktop. None of the Microsoft literature I can find seems to indicate this; even their own Development tools (Visual Studio 2013) only provide a few templates for creating Modern UI applications and they are not the default option (The default project type being WPF, which creates desktop applications)
You could plug in most mobile devices to a PC well before the Modern UI. Touch screen PC's were available long before the Modern UI.
Using a standard desktop application with a touch-screen is not exactly a friendly experience. Buttons that are otherwise easy to click with a mouse pointer are tiny when you have to press them with a finger. scrollbars have even smaller elevators and arrows, and the paradigms of dragging do not always translate to a touchscreen very well.
So yes, you are correct that Touch Screen PCs were available before Windows 8 was released. That much is obvious.
No desktop Operating System has had any particularly large amount of thought put into how it is used with a touch screen. Windows 7 made it's changes to the taskbar but the fact they are easier to tap is probably a side-effect and the real reason was a desktop-oriented design decision. It's fundamentally the same as when the mouse was introduced. Operating Systems and Application 'supported' them by having very clunky usage cases that basically just acted like the mouse was using the arrow keys and invoking program actions; for example you click on a menu and it drops down. Same for Touch screens- it basically just pretended it was a mouse. You could not perform multi-finger gestures or touch-screen specific capabilities simply because the Application pretended the touch-screen was just your everyday mouse, just as early applications pretended a mouse was just performing certain keystrokes. It was not until we had operating systems that took full advantage of the unique capabilities of the mouse (Mac OS) that it's potential for usability was truly unleashed. I think it's the same thing now for touch-screens, but Microsoft is combining two efforts- the threshold effort to merge multiple codebases and allow applications to target multiple platforms at the same time, as well as providing full support for touch-screens and their own features, rather than just pretending it's a mouse like previous versions or other Operating Systems often do, and implementing "touchscreen" features such as gestures by simply making them Mouse-centric capabilities (OS Lion, as I recall).
Microsofts' vision of the future is "one Operating System to rule them all" and is driven by the Modern UI, not the Desktop.
Threshold (the effort to provide a single target that applications can develop against to run on multiple platforms) is complemented by the Modern UI by virtue of the fact that Phones, tablets, and other devices simply can't run x86 applications, and the desktop-centric UI Design is abysmal to use in that environment. Microsoft has been writing Operating Systems for handhelds and pen and touchscreen devices pretty much since they came out and they learned that applying their desktop-oriented paradigms to touch or pen-centric devices with limited user-input is a very poor approach. Modern UI is essentially the design concepts of the Windows Phone OS's Silverlight/XAML expanded and made available to desktop machines. I don't think there is a very string basis on which to assert that Microsoft intends to completely replace the x86/x64 Desktop/windowed applications, since that basis is essentially that apps written for the phone or tablet will also run on the desktop OS.
"The full capabilities of Windows will continue to be available to you, including the Windows Explorer and Desktop"
-Julie Larson-Green, Corporate Vice President of Windows Experience Team on a news article pre-BUILD 2013.
Many articles in my searches make the implication- or state outright, that the capability to run standard desktop applications is only available for "compatibility" or it is now "legacy". This makes the confusion a bit understandable- however, This contradicts pretty much every official statement that I can find from Microsoft officials as well as their actions.
As far as I'm concerned the "Start Screen" is basically just the replacement for the start menu. When you open Start you get taken to the start screen; when you launch something you either stay within the Modern UI environment (if you launch a Store App) or you are taken back to the desktop; semantically equivalent to the previous start menu. It kind of merges a fully-folded out All Programs Menu with the Win7 Start Menu and fills the screen. Microsoft's other applications (Visual Studio, Office, SQL Server) are all still standard desktop applications. Fundamentally, the Modern UI is designed primarily for content consumption. Whereas the desktop can do both.
Since Visual Studio is never going to have a App version, it's simply ridiculous to suggest that the capability to run desktop applications is maintained purely for compatibility or legacy purposes.