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.
The 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.