Yes: Money
Ah yes, the thing Microsoft has so little of.
Supporting one system for now might help (e.g. only SteamDeck) but Iassume putting the package there makes it generally available for all users?
It would be available for all Linux users, Flatpak runtimes are a singular target to develop for, desktop Linux users usually are fine with 'only distribution XYZ supported, you're on your own for everything else', and Microsoft could even bundle a Proton-like compatibility layer based on actual Windows code and not allow more than just streaming.
As for only streaming: They make Edge for Linux already but rely on unpaid members of the Flatpak community to package Edge when they could just do it by themselves. Plenty of Linux expertise is already at Microsoft.