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.

Rumor has it that crush and love increase chemistry, which might be the explanation for the First Kiss event.

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.