I guess the question boils down to: “Is an application distributed via the Microsoft Store allowed to come along with a “custom installer” which installs it at any given location of its choice (like the Community folder)?”
If the answer is “yes” then there would be nothing preventing an add-on developer selling her products via the Microsoft Store instead of the in-game marketplace.
Disclaimer: I don’t know the rules of the Microsoft Store.
Update: the next question would then be: “Is it actually possible to sell non-standalone products (only runnable together with some separately sold product like MSFS) in the Microsoft Store?” - Again, I don’t know the answer, but I assume the answer would be “yes”.