Apktool intentionally doesn't handle Carbon/Liquid. There was a commit adding resource qualifiers for something called "inverted" mode. Apktool cannot follow every ROM's choice to modify resource qualifiers, as some may break legacy support. This specific change you are talking about, looks like it patches cleanly, but I don't know if its Apktool's job to patch itself for every ROM's change.
These changes aren't just "change x and rebuild". You have to rebuild aapt and apktool for these changes, since aapt handles the rebuild. Building aapt for 3 different platforms to test these changes isn't fun nor easy.
The best bet would be to re-engineer an aapt binary that ignores things it doesn't understand, but then how would we detect errors
Trust me, I've been thinking of ways to make this easier for everyone, and there just isn't a good extensible solution yet.