Thief kits, skill points, and Shadowkeeper

I like to use Shadowkeeper to give NPCs some kits that they wouldn't normally have, but there seems to be a bit of a problem: if I use it to turn a regular thief into an assassin or bounty hunter, they keep getting the 25 points the vanilla thief gets, even though they should only get 15 or 20 points, respectively.

What's up with that and how is it fixed? It makes me feel like I was cheating.