I’m afraid you need to find the offending configuration option. Maybe it’s an application that starts automatically, maybe it’s the KDE display configuration, or maybe it’s something else.
The Xorg configuration I posted should ignore the GTX 1080 altogether. If you delete it, and boot without any display related Xorg configuration files, I believe both should be automatically configured, and you should be able to use both.
I was able to get the 3090 to output to screen on my original profile by deleting the contents in ~/.local/share/kscreen and then use the xorg config pobrn posted above and replacing the PCI bus to use the 3090. Still didn’t get the 1080 to output alongside the 3090 but I plan to use it for a passthrough regardless. Adding it and a screen to the xorg config will most likely get it to output just fine.
Thanks for the help.