The Windows Store version doesn't register itself as a handler for the .mscz format
I installed MuseScore from the Windows Store (https://www.microsoft.com/en-us/store/p/musescore-2/9p0cnr9rwzsx). When I try to open a .mscz file, the "How do you want to open this file?' list doesn't include MuseScore. In Settings\Apps\Default apps\Set defaults by app (Control Panel\All Control Panel Items\Default Programs\Set Default Programs), MuseScore is not listed at all.
The end result is that there is no way to set the file association of .mscz files to the Windows Store version of MuseScore short of some obscure and complicated registry tweakery.