Purchase Windows 10 Pro Microsoft Store
Gro Bert
Another thing that may be a benefit for you is that you also get the game for xbox plataform. Last that comes to mind is that you get family sharing wich let you play at the same time with one family member. I never tested it with MSFS, but it worked OK with Sea of Thieves
Maybe those who prefer steam can tell you some benefits of buying in that plataform to help you in your decision.
With the Steam version you can edit the config files and all other assets without getting locked out by windows. Windows store installs to protected directories which is a pita. With the Steam version you can easily move stuff around after installing with a couple symbolic links or simply edit the packages folder path in usercfg.opt
Unfortunately switching between the two has not been made easy and if you already bought stuff on the market place for the windows store (gamepass) version, you might not be able to use that on the Steam version.
For how it runs, no difference. Steam only installs the installer, which installs the game (just not to off limits gibberish directories). Updates to the installer launch a few hours later on Steam, so if you need the cutting edge update straight away, the windows store is a few hours ahead.
Just kidding. Buy from wherever you like. But I bought it from MS Store because I wanted the full amount of money to go directly to the publishers and developers, whereas Steam will take a cut of the money.
After I felt the general tone there I decided that MS Store is safer. I am not saying it is a rational decision, but games sold with their own launcher (Rockstar, Ubi) usually benefit very little from Steam and might create problems of their own.
Havin tested both, id recommend to take the Steam version.
On MS Store you are not getting acess to all the files and therefore you can be limited when using external 3rd party software like ReShade for example.
I think Microsoft has sorted most or all of this but a number of people had problems before with the Microsoft store getting confused on if they had bought upper tier packages of FS2020. One guy even abandoned his purchase on the Microsoft store and bought again on Steam to be able to access the premium planes.