Stardock has shown there is no detriment to adding the start menu back, restoring windowing, and integrating apps of all types to the taskbar.
The only reason I can fathom on why they want to two worlds separate [...]
I think one detriment of supporting this officially is that developers would then be expected to design and test for resizing to resolutions below 1024x768. One of the goals of the WinStore app model was to reduce the amount of stuff like that developers had to worry about (because they thought issues like this were one of the reasons developers were drawn away from PC and towards platforms like iOS).
Now I'm actually positively surprised by how well the apps do resize despite this. I guess since the WWA/XAML frameworks and controls are designed to adaptively scale, the apps get a fair amount of sensible resizing behavior for free even when not designed or tested for it. However, obviously there are some significant glitches and brokenness here and there (look at the chart control in the Bing weather app for example), that would take extra work for the developer to fix (and remember the cliché that the last 20% of polish takes 80% of the effort ...) and while it's OK for a third-party mod to expose behavior like this, I think it's much too flaky for an officially supported feature (OK, the apps are flaky in some ways already, but this would make them EVEN MORE flaky).
Personally I think a good approach for an official feature like this would be to just leave it up to developers whether their particular app supports it or not, and hide/disable the UI control to change modes for apps that don't. Then devs who don't want to worry about supporting resolutions under 1024x768 still don't have to, and devs who think their userbase includes a lot of people interested in using the app on the desktop can do the work to support it properly. (and people who really want to resize apps that don't officially support it can still use third-party mods to do it without putting an expectation burden on the developer ...) Additionally if apps know whether they're running on the desktop or not they can make some appropriate modifications to their UI - e.g. it's silly having both window chrome with a title that says "Store" and a giant header that says "Store" (well, tbh I think it's silly having a giant header that says "Store" even when the store is running fullscreen, but it's doubly silly on the desktop).