Its my understanding that for windows store installed desktop applications, users wont have access to the folder that MB is installed.
So that means to install a new plugin, skin, theater mode skin or visualiser cannot be acheived using older MB versions. It also means there will be no portable version from the Windows store.
What i have done is include an "Add" button for each of the customisation types. So to add a new plugin there is an "Add Plugin" button. And for skins, its in the View/ Skin menu, etc. These buttons are available whether you would download MB from the windows store or you update MB the usual way you do now.
Any customisations added this way get installed to the user/appdata/roaming/MusicBee folder.
If you do this using the portable version of MB, the new customisations are saved to the existing folders ie. there is no change
Because you already have a number of customisations already installed with MB and ones you installed yourself, the existing customisation folders will continue to work - its only the new customisations that are added using the "Add xxxx" buttons that will be saved to the appData folder.
Perhaps for a future MB version, i will include a Customisations panel or section in the preferences panel so its all in one place.