"The MBR is not a standard."
Standard: "Used or accepted as normal or average"
What do 90% of all computers use? an MBR. GPT is only used in very specific circumstances. And, even a GPT partitioned drive will have a valid MBR, as I noted before. Therefore an MBR is a given for any windows system (as well as many other systems). If that's not "standard" I don't know what is. Is it an ISO standard? No. That's irrelevant anyway. Warranted the actual boot code is probably different (in fact, it is, I just checked, using the excellent MBRUTIL), but the actual layout of the MBR between XP and Vista didn't change,and the rest of the MBR aside from the boot code itself, is the same. The fact that the boot code actually changed between versions is hardly surprising; DOS uses a different MBR than NT which uses different MBR boot code than Vista/7, which in turn use different MBR bootcode than BSD or GRUB/LILO; this is hardly something work squawking so loudly about. Either way, The differences between XP and Vista's MBR reside plainly in the boot code, and the actual way data is stored is unchanged.
FDISK isn't going to rewrite the boot code within the MBR of a system unless told to do so using the /MBR switch, or if there is no MBR present. This is well documented
here.
Repartitioning with Fdisk does not rewrite this information.
Naturally, third party tools from that era may act differently, but nothing posted by the OP leads me to think they plan on running anything but FDISK. The bigger problem is that MS-DOS wouldn't see the drive since it is attached through USB, and it seems more like the desire to do this is a result more of a misunderstanding of the terms involved as Salmon Trout pointed out.
From the sounds of things, they don't actually have any functionality problems with the drive at all, and their desire to fiddle about with it is purely on the basis that they have a partition set active while the others are not. Considering the fact that the active partition only determines what is booted from, and it's difficult to tell if they intend to try to boot from the drive.