My thoughts sans further or deeper rules clarifications ...
The Skills thingie looks to be splitable into 4 categories.
High Caste can use High and Mid skills and still retain Honor+
High Caste can use High, Mid and Low skills , and not be Honor+
Low Caste can use Low and Mid skills, and largely ignore trying to be Honor+
Mid Caste can use Mid but not Low, and still retain Honor+
So to simplify they can be called: Low , Mid , High , High+Honor
... each description implying the more detailed stuff.
So then the High Caste have to follow the Clan system.
Add the 1 specific Class skill, already available to High, except Scorpion Bluff.
Take 1 of the Clan Ancestor feats instead of Human Bonus.
Some limited # of NPCs (not many) have to deal with the Favored Class nerf.
Not sure how much these details matter, just that they exist.
(so far only in my kitty avatar's vacuum)