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.