Ok, that's really quite strange as every update that I have had until SU5 did as you describe and took me to the MS store *, to the MSFS2020 page where it recognized an update was available and downloaded the first GB or so, then the game started in the new version and the bulk of the download was done from within the game, whereas since SU5 the two small updates took me to the store (homepage, not MSFS page) and the updates happened in the background, and this last one did not take me to the store but opened the game already updated (the version number was new) and then the game started and the major part of the download happened as it always does within the game. So seemingly the opposite to your experience!
As to Xbox stuff... I do not and have never owned an Xbox, essentially I play the very few games I play on a PC. When I purchased MSFS (on release and from the MS store) I had to make an Xbox / Windows account in order to play it as it's always been an Xbox game - it's the first splash screen that comes up when the game boots. I guess that is why I needed the Xbox app as I never voluntarily / consciously downloaded it, and it just sits on my PC doing nothing - well it obviously does something, but no idea what, other than the fact that I'm logged into my Xbox / MS account...

And this was at release, way before the actual Xbox release of the game.
* Edit - Previously I would start the game and it would come up with a screen saying a mandatory update was available / required, clicking on that would open the store and the core update was downloaded there, within the store. After that, clicking play in the store the game would open and then the subsequent larger downloads happened in-game.