Ah, understood. 
That part that you are talking about (comes from the client, MS Store/Steam) is the installer. 2nd part (in-game) would be any core updates. And yes, those you can’t stop (well you can, but it only pauses it until you come back to finish it).
But I hear you, it would be nice to pause it so you can play as they take forever to download. Then come back to install to keep current with what/may be coded in the cloud for it to work. There is a wishlist on this if you want to up vote and contribute too:
https://forums.flightsimulator.com/t/dont-force-users-to-update/274148
There’s some other wishlist topics about this as well:
Search results for ‘updates category:163’ - Microsoft Flight Simulator Forums