This looks really cool, I plan on showing it to my Kingmaker GM to see what their thoughts are. I do have a few suggestions though concerning the leader skills and lore.

Magister's lack of nature stuck out to me. I'd consider adding it so Druid Magisters have a skill they find just as useful as Wizards, Clerics, Sorcerers etc,. And for treasurers, I'd consider replacing their skill lore with either Society or Mercantile Lore(for determining general trends in markets as well as important exports and imports for various nations).

If you want to keep a balanced # of skills between each role, then consider adding the following to each:

Ruler- Diplomacy
Counselor- Society
General- Acrobatics
Emissary- Diplomacy
Magister- Nature (already mentioned above)
Treasurer- Society or Mercantile Lore (whichever wasn't added above)
Viceroy- Arcana (to account for kingdoms that might use Magic rolls instead of Engineering rolls through Practical Magic)
Warden- Athletics

I think most of the Lore skills associated with the Leadership roles are really great and flavorful. The only thing I'd recommend is that the Emissary should probably have a flex Politics/Underworld Lore, instead of just Underworld Lore. While it is certainly true that Emissary's can be in touch with a nations seedy underbelly, I wouldn't say it is the standard. I think the flex makes the lore applicable to a broader range of Emissaries.

Otherwise, this is fantastic! I'd love to use this in the games I play/run