I’ve been using Fedora Workstation for a couple of years now, and I was happy to see global shorcuts coming to GNOME 48 under wayland. I usually will test the next version of Fedora in a VM before updating and I will also wait about a month after new releases of GNOME/Fedora in order for any major bugs to be worked out before updating. When I was trying out GNOME 48 in a VM, I got the global shortcuts popup on certain windows (ie: Discord, OBS etc.). However, after upgrading to Fedora 42 and GNOME 48, I haven’t ever seen a popup to enable global shortcuts in any applications. As far as I can tell, there isn’t any way to enable/configure these shortcuts within GNOME. There is probably a way to do it in the terminal, but since this a new feature I’m having trouble finding documentation on how exactly to remedy this issue I’m having. I’ve waited for quite a bit now thinking this was a bug that would get patched out, but I don’t see anyone else talking about this anywhere.
So, I made the same post on the GNOME discourse forums, and the only conclusion that I’ve come to now is that this is due to the developers of the applications I want global shortcuts in not having them enabled anymore (at least right now). They will potentially get added again in the future.
Out of curiosity, on my F42 Silverblue machine, I have installed as Flatpak the app demoed in one of the replies to your post in GNOME’s Discourse as an example to be having global shortcuts implemented (com.belmoussaoui.ashpd.demo), and sure enough, it didn’t present the option to configure global shortcuts at launch, neither can they be configured in Settings → Apps menu.
You could install GNOME OS Nightly in a VM and check if it is working there. If it is, than it might be related to Fedora 42 after all.