I know people say never to run GUI programs as Root but there are some programs I use that are faster to get things done. I used to run KDE System Settings as root and simply apply it with a click. I never had problems when using Manjaro KDE and Kubuntu.

I used to simply clone one of the default QT/GTK themes, tweaked the color codes, and then moved them to /usr/share/color-schemes/ for QT & /usr/share/themes/ for GTK
The command I would use was:

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$ kdesu systemsettings5

KDE developers have since removed the option to use kdesu and I was wondering how I can change the default Root themes for QT and GTK apps. I don't plan on using themes from the KDE Store since those tend to have outdated metadata.

I was thinking maybe adding a file in /root/.themes for GTK Themes?

As for file locations, I assume that the root user's home directory is /root/, so for any file locations which reference '~' or $HOME you should be able to just replace those with /root/ to get the root user's location for that file.

Also, even if kdesu isn't available, you can still use su and/or sudo to run stuff.