So I finished making a custom henchman and went to test it in-game, and noticed that his attributes were much higher than they should be. After some testing I determined that any (non-custom) level 3 henchman gets +1 to ALL of the stats that are not modified by his or her preview screen. This increases to +2 when hiring a level 5 henchman. It's easy to spot this by finding one with no modifiers to intelligence and seeing them have 7 intelligence.

On a probably-unrelated note, my Jahan seems to have 1 more INT than he ought to at level 6.