I have a few reasons to think that Microsoft does not intend to replace the standard Desktop.
The main one is that Windows Store applications- all of them- basically any program that runs with the Modern UI, have ridiculously heavy restrictions. If what you claim was true, than the end result would be that no applications would be able to access the local system, at all. a Modern UI application cannot read or write to the local hard drive, it cannot even use third-party libraries (I know this since I wanted to make a Store App that used Postgres but of course I couldn't references the postgres library). Fact is that All Modern UI applications are weaker than any desktop counterpart. The reason for both of these are simple: Modern UI applications are not designed for use on PCs, they are designed for tablets and smartphones- both of which have had similar restrictions on software that runs on them for quite some time.
Additionally, Consider the applications that Microsoft currently offers.
Now consider how many of those have Modern UI equivalents. I can't think of many, to be honest; Office 2013 is still a standard x86 and x64 Windows Application and runs on the desktop. What's my point? Windows 95 was the last major shift. They introduced the Taskbar, 32-bit Software, the Start Menu, and effectively a entirely new way of interacting with the Operating System. It is equivalent- in almost every way I can think of- to what is claimed through your theory with Windows 8- a complete rework of how the System is used.
Microsoft had a version of Word that ran on Windows 95, using Native Windows 95 components and shell capabilities, on the same say that Windows 95 was released to the general public- Office 95 was released on the same day as Windows 95, on August 24, 1995.
In that case Microsoft was seeking to replace the old way of doing things.
If they sought to do the same thing with Windows 8, why has there not been a version of any Office program written for this so-called replacement, almost two years after that version was released? Same for their other programs; Microsoft released versions of their Development Tools that ran on Windows 95 as Windows 95 programs; they released versions of their Browser, SQL Server, and innumerable other software packages to run on Windows 95 as native Windows 95, 32-bit applications.
In contrast their "support" in the same way of the Modern UI has been sparse. Only thing I can think of is Internet Explorer.
That's why I don't think that is at all their goal. Because it has been their goal to do this sort of thing in the past and they have been quick and decisive in pushing it forward. They seeded the new environment of Windows 95 with several of their flagship products. There is no "flagship support" from Microsoft's largest product suites for Windows 8's Modern UI. Which to me means that the core premise that they want to completely replace it is incorrect. (or, they forgot how to perform a declarative switch over like they did with Windows 95).
