No offence, but that's pretty obvious. Potted history of my experience with WF on Steam Deck below:
I prefer to play most shooters with KB+M if possible, so my first attempt (after some basic testing to make sure WF runs at all on Deck) was to switch to Desktop Mode and launch from outside of BPM. It still refused to let me navigate any menus with the KB+M, going so far as to completely break the login screen. Launching from BPM or Game Mode was at least functional thanks to the on-screen keyboard, but still forced me to navigate menus with the controller, and more-or-less broke text chat to the point that trading with other players became impossible. The workaround I ended up using was to link the WF executable as a "non-steam game shortcut" and use a launch option to bypass the Steam Input API. (See the link in my last post)
As best I can tell, WF doesn't care if it's launched from BPM. It only checks once on startup to see if a controller is plugged in, and if so, assumes the player will be using that and locks itself into controller mode. And since the Steam Deck has a controller built-in that obviously can't be disconnected, that causes issues.
Later on I decided to just use Windows for WF going forward due to AlecaFrame compatibility, and uninstalled WF from the Deck, including that workaround. At time of writing, I'm away from my main gaming rig for a few weeks, so I'm having to use the Deck again for the Recall: Ten-Zero event, and put up with the borderline-busted controller implementation.
It's a shame, because aside from these controller issues, WF actually runs very well on Steam Deck. If DE were to fix it so that KB+M can navigate menus on Deck without a workaround, and if AlecaFrame were to add Linux support, I'd be more than happy to exclusively play it on Deck, and recommend that others do the same.