Quite intresting! thanks for the help!

Tandemaus can get to 99% they function like normal pokemon

Yup, just like regular pokemon they will pair together to make 90%+ pairs making their maximum 99%~

I can get 90 and 91 with a poly of Axew x Charizard and Charizard x Nidoqueen. I'm thinking about swapping out Charizard for another fire type and just doing Axew x Nido since logic says it could work, but I'm having trouble finding a pair with a base compatibility high enough that I can raise it to 90+ after getting the other factors up. Did I just get lucky with this Charizard that he likes both or do I just need to keep looking and trying out more Axew x Nido couples? I've also considered new pairs for pure dragon gems and poison gems, but my options are very limited.

If I breed a Flabebe with a Spritzee instead of a Ditto, would I actually get more Flabebe eggs overall? Or would I get half Spritzee half Flabebe? And is there any benefit to having a breeding pair over 100%?

Do the non-Ditto pair. You will get eggs from both, but it's a higher compatibility (possibly) and therefore more eggs to be made since you can't make a Ditto egg and it just skips the breeding if the coin flip turns up Ditto. But what you really want is to breed two Flabebe with 2 different owners and neither be you. I'll what I have or can find if you're interested. As far as >100% pairs, I'd have to try some experimenting, but anything over 100 may be a chance of a second egg from the same breeding, if I had to make a guess. Or it's just super guaranteed to have an egg and you can Red Giga them and not have to worry about giving them a rest for a while.

Flabebe is a monogender pokemon so you cannot get two to breed together. Ultimately because it is monogender (female only) you will be only getting 50/50 breeding one way or another so breeding with a spritzee at 85% vs a ditto at whatever max % that is (i cannot recall off the top of my head) is going to be more or less the same in terms of egg production, the higher of the two will produce more eggs overall however. There is no benefits of having a pair over 100% with happiness, you aren't getting a 20% chance of breeding two eggs it's simply a buffer for if you are using the red giga to breed before you start losing breeding chances It's been a while since I made any attempts to make pairs of pokemon that aren't two of the same species line, but I recall the max chances (assuming same body shape) is somewhere in the 70-80% range, you will not be getting in the high 90s with two different species lines of pokemon.

Ah. That's one of them I'm less familiar with. Sorry. Isn't a Ditto pair going to have a lower % and half as many eggs as a Flabritzee pair, though? If you all already agreed on that, that's fine, but it could be worth considering multi-egg batches for pairs that have high enough compatibility. Is that base compatibility or max compatibility? Cuz I can show you a Butterfree x Beedrill pair with 102% compatibility after all the math and a 85% base. :3