The fact that Addon Linker, at the community folder puts shortcuts to the mods, and not the mods themselves, only means that MSFS looks for the mods via the shortcuts, but it has access to them, and are indeed active that way. So IMHO, should the content of the community folder be some kind of menace for MSFS updates, there is no diference about using or not using the Addon Linker.-
But the fact is that mods doesnt modify or overwrite any Asobo file, so in case of having problems, the fix is cleaning or moving away the mods from the Community folder. As far as I know, MSFS just allows mods to take precedence, if they improve or modify any Adobo file, without letting any modifications to the original one.