My apologies if this has already been answered: The Red G doubles the breeding chance. And the first time two mons see each other - that is their set % Say I put a pair in the first time with the Red G, and it comes out at 98% - is this now the locked figure or is it really 49%?

The Red Gigaremo wording is not great. It does 'double your chances' but not by affecting your matchup percentage in any way. That is set based on the factors listed in this Guide. What it really does is halve the number of interactions you make before it checks to see if an egg was bred, from 64 interactions down to 32. So the Base matchup % you see when you First put two pokes in the Daycare together is Their percentage.

So it is up to random chance on whether or not I get a 99% pair? Even on exclusives like Cactaboo?

Yes, it's random. Just keep trying. Especially with Pokemon you receive in trades.

will pairing up two pokemon from the same line but different species affect the breeding percentage? say I have a primarina and a popplio I'm gonna evolve later. will the fact that they're different species override the possible 99% chance they have if evolved fully?

Once two pokemon have "seen" each other the breeding % does not change. This includes if one or both of the pokemon in the pair are evolved. Pokemon of the same species can always be paired regardless of evolution as well.

This has likely been answered already but I'm having a hard time finding it in all these posts? 😅 I'm trying to match Froslass and Ralts to breed Snoralts. The highest compatibility pair I've made so far is 60%, is that the max?

Not sure about that cross-bred pair max, but being a Variant, you can get 90%+ pairs (max 99%) of snoralt + snoralt, if you want :-)