I am not an expert to say that what you are trying to do is either impossible or near impossible. I guess that it will be a challenge even for an expert. The question is who want to invest their precious time to experiments on something that has no real benefit ( other than for the fun and satisfaction in doing so ).
Btw, NT5 family OS supports changing the root folder name of Windows. Instead of the standard "Windows", you can use your own custom name. I am not sure whether it is still possible with NT6. I think "Windows" is hard coded in "Bootmgr" and other OS loading components.
Well, I consider myself as some sort of expert in bad in good and no I don't see it as impossible at all in fact I got this working at UAS USB 3rd partition currently. I am clad to invest my time to build this as you can imaging the idea of NT6.x being installed x64/ia32 EFI compatible and same time supporting x86 old systems live from any media don't see who wouldn't be.
I don't think you are correct about bootmgr having hardcoded "\Windows" and I believe it being only at registry after winload.exe/efi is directed by BCD (which, yes, is insanity level to be started to be modified because of so many microsoft misuses of %SystemRoot% and %WINDIR%). I even believe this might be able to be build by unattended.xml or autounattended.xml as an automated process,
Another option might be using VHD files. You can create two VHD files on the same partition and install x86 and x64 versions to them. This way file/folder name conflicts can be avoided.
Yeah, VHD and basically 2 different partitions is of course a choice, but that again negates the whole idea of having hardlinked x86 content from x64 OS to remove duplicates from both OS, which reduces 2 OS size insanely and right kind of tweaking with NTFS compression brings this even further in size. I counted ideal system using around 11GB in full x86-x64 it could be half of that without .NET as live system.
All above concepts should be in one hell of an interest to people who builds systems like 'Yumi', WINNTSETUP, RMprepUSB, WIM toolkik and other such software (only few to mention).
(In the end we are talking with current hardware All-OS flash media from DOS + 2xx Windows versions to about same amount of core linux distributions all compressed to single archive, differentially and mountable/bootable directly from archive at any environment. To archive this we are too early at both linux and windows side and probably neither never ever live peacefully together which says we need new WIM style standard to market from opensource capable of NTFS and EXT2-4).