Good catch. This will be fixed in next release.
I cannot enforce this, because tags subsystem goes beyond Finder. It is a system-level feature. Right now colored label is defined as color of the last tag applied. I can imagine some external utility sitting in background and watching filesystem events and enforcing some rule like ‘keep only most recent tag’ or something similar. But this is beyond scope of TotalFinder I guess.
Tag colors can be possibly redefined via ~/Library/Preferences/com.apple.labels.plist. But this is probably legacy feature which will go away in the next OS release. I don’t know more details and I wasn’t able to google some additional info.