I think they got the nvidia driver accumulation thing straightened out. On Fedora 40, I had it automatically remove a bunch of older versions and now it only lists the 64 and 32 bit versions I expect it to.
$ flatpak list | grep nvidia
nvidia-550-76 org.freedesktop.Platform.GL.nvidia-550-76 1.4 system
nvidia-550-76 org.freedesktop.Platform.GL32.nvidia-550-76 1.4 system
Edit: looks like it’s fixed by this.
Nope, not at all. Silverblue here (GNOME), and the upgrade went smooth, nvidia drivers and all.