I guess maybe the Windows App Store version installs hardware packages to a different location than C:\Users\USER\AppData\Local\Arduino15\packages\arduino\hardware\samd. You could try to find that location by doing this:
- Tools > Board Arduino MKRZero
- File > Examples > SPI > BarometricPressureSensor
- Sketch > Show Sketch Folder
It's possible that the problem behind your "board... is unknown" error will prevent that from working.