I have the same problem (`bluefin-dx-nvidia:stable` : can't open some native apps anymore - Bluefin and Aurora - Universal Blue)
I am on bluefin-dx-stable:stable (Universal Blue image on top of Fedora Silverblue) which is on Fedora 40 as of now
Is ~/.config/environment.d/gsk.conf a new file in Fedora 41 ?