I'm not sure if this is something I can fix on my end but any GUI exclusively to AE2 doesn't switch to dark mode, all it does is change the font colour.

A stop-gap measure would be giving a denylist for UIs that don't work the best with the dark mode on, as requested in #13...

I mentioned the issue here in the ATM8 issues, but I also noticed that DME does work in ME Pattern Access Terminal but not the other ae2 UIs

AppliedEnergistics/Applied-Energistics-2#6726

Once DarkModeEverywhere is available for Minecraft version 1.19.4, the AE2 devs will look into it :)

I can proudly say that there are now releases for 1.18.2, 1.19.2, 1.19.4, and 1.20.1 that are all compatible with AE2.
If you have any further problems, please drop a comment here <3