This happens because MSFS is not a true full screen but a borderless window. Current Windows versions already handle a borderless window as full screen, so in terms of performance they are basically the same thing, but rendering priority still depends on which app window is active, so which one gets the mouse clicks or was switched by means of ALT-Tab, because MSFS is still a windowed app as the rest of standard Windows apps. Anytime MSFS does not have the priority what you are renderering indeed is the Windows desktop, that still contains MSFS as a visible windowed app. For MSFS to take rendering priority you need to click with mouse anywhere on the MSFS screen if you have multiple screens or switch to it using ALT-Tab. If you see the Windows mouse pointer on MSFS instead of the native MSFS mouse pointer (which is different and disappears after some time) then MSFS is not the active window.
You can easily check that effect if you have two monitors, you are able to set their refresh to something higher than 60 Hz as MSFS normally runs below 60 FPS (so for instance set 120 Hz) and you run game only at one of them. Open developer mode FPS counter and you will see that if you click on the second monitor (to interact with explorer or any other regular app) MSFS FPS counter will display 120 FPS, which are the FPS the Windows desktop is being rendered at, even if MSFS is still visible on the other monitor. However clicking back on game window will drop FPS back to 60 FPS or below as then MSFS is getting the priority. You can also check that with one monitor only running at 60 Hz (or any other refresh) by simply putting an small internet explorer window on top of game. While explorer is active game will display 60 FPS or the equivalent figure for your refresh and closing explorer will not change that figure. Until you click back on MSFS window the FPS value won´t go back to something below 60 FPS or the equivalent figure for your refresh.
This behaviour can easily confuse people as they may think game is running much better that it really does because, for instance, while desktop is getting priority you may not be main thread limited as FPS counter is giving a false reading and it´s always steady at its max possible FPS value. It also appears that game is running smoother, but this isn´t the case. Remember the basic rule: if you see the standard Windows mouse pointer you are not getting the real game readings in the game FPS counter.
Cheers