I am using Fedora 34 64-bit with Gnome 40.7 and Wayland.
I have a Mesa Intel® UHD Graphics 630 (CML GT2) / AMD® Verde graphics setup. This was working a few months ago without issues. It is possible one of the upgrades in the past two months broke something, but I also took the graphics card out, used Fedora, and then put it back in which may have caused the issue.
Windows 10 does not have this issue.
Start the system from a shutdown.
The desktop spills over the screen driven by the AMD® Verde (the window dimensions are larger than the screen dimensions), but there is nothing wrong with the screen driven by the Mesa Intel® UHD Graphics 630 (CML GT2) .
Open the display settings and apply literally any change to the screen driven by the AMD® Verde. Then switch the setting back to what it was and apply, therefore the settings are exactly the same as they were during startup. The screen driven by AMD® Verde now has the correct desktop dimensions.
The display is sized/configured initially by the data received from the monitor.
Your post says nothing about the monitor you are using but I often see exactly what you describe when switching from a dedicated monitor to a tv for the display. The fix there has been to set the tv to not overscan. Thus the fix has been in the tv/monitor and not in fedora itself.
May be you could also try to toggle “Adjust for TV” option. Go to Gnome Settings → Displays, then select the appropriate monitor and at bottom option there should be an option “Adjust for TV” then toggle it on or off.