Thanks! I managed to make it work. For all folks asking: Can I run VR with HTC XR Elite glasses on MSFS bought from Microsoft Store, the answer is yes!
You need to:
- Launch Vive streaming Hub app and pair it with VR glasses
- Launch SteamVR, go to Settings > Developer > Current OpenXR runtime > SteamVR needs to be active
- Turn on your VR headset
- In desktop, open MSFS, Options > General > VR Mode > Switch to VR
- Put on your XR Elite, go to Library > installed apps from PC > SteamVR and you should be in-game now