Good question, and I think that your initial answer is technically correct. However, I also agree that it doesn't make a lot of sense. After all, a functional specialization grants a bonus for all themes within that function, so in makes sense that a thematic specialization should grant bonuses to all functions within that theme. In this case, I would say that a thematic complexity bonus also improves crafting strength within the theme, and a thematic control bonus boosts frequency.
I think I would be very careful (ie, I wouldn't allow it) about allowing larger bonuses within a ... er ... "thematic function" or "functional theme". That would probably lead to overly powerful combinations, especially with respect to thematic crafting.