I'm fairly certain there are things I haven't explored that affect the chemistry calculations.

I have twice seen sims go from -1 bolts to +1 bolts after sharing First Kiss. It's possible the First Kiss memory adds a bolt and, if its the first for both then that's 2 bolts. I haven't done experiments to test this.

Gender preference could affect chemistry in more than just an on/off fashion. Since gender preference ranges from -1000 to +1000 it's possible higher preference means higher chemistry.

Fitness preference may alter attraction. It's another hidden attribute of all sims that I've never understood.

I read something that claimed interests affect chemistry. Frankly I'm doubtful because it would have introduced inconsistancy to my existing test results. I haven't actually checked interests though so I could be wrong.