https://www.gamedeveloper.com/pc/besiege-devs-spotlight-why-some-games-can-t-work-well-on-steam-deck
PCcontroller support is just one hurdle games like Besiege would need to overcome; Spiderling Studios says it's not as simple as copy-and-pasting the console's code.
Sounds more like its just not financially smart to add compatibility for the Steam Deck. Remaking the game for a console version is fine, since they attract a massive amount of sales to pay for said upgrade. They won't make nearly as much money by just helping out us small 4%'s.
As far as I'm aware, no other developer has had to entirely redesign their game just to add controller support.
I like that the answer boils down to: because the developer dont want to make it work. Its the most honest answer and im totally fine with it. If its because they dont want to do it because of finances or like in this case because they actually do completely different versions for their controller releases. It paints the correct picture that a game doesnt support a platform not the other way around