I’m not sure where to file a ticket about this, because I’m not sure what the root cause likely is. Does the gnome-nightly repo need a master version? Should some part of this be trying to install 25.08 instead? Should I be doing something special in my CI config?
I think you’re running into a known flatpak (or flatpak-builder) bug that just hasn’t been addressed for years. It falsely tells you it wants to use the same branch on the extension as the sdk, but it needs the same version as the freedesktop-sdk the current gnome runtime is based on.
Does installing the 25.08 golang extension resolve this?