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"Now, there is also a situation where you may have two Metro-applications side-by-side, but then you need to switch to a desktop-application briefly and back: will your two Metro-applications still be side-by-side or will you have to adjust them again? "
In this case the desktop would normally take the place of the primary Metro style app (so the snapped one would still be there on the side) and then when you switched back to that app it'd take the place of the desktop again, so you'd be OK. I think this would generally work for brief use. If you felt the need to fully maximize the desktop (and unsnap the other Metro style app) you'd have to reconfigure them, though.
The main gripe I do have is that there's no convenient way to start a new Metro style app in the snapped view, unless it happens to be an app you've recently used (in which case you can drag it from the switcher). You have to go to start, tap on the tile for the new app -> it starts fullscreen so you have to bring in the previous app snapped and then move the separator (because there's no way to bring an app directly into "filled" state).