#1. I would say it all evens out. I would say for a while anyway, the committee has not really cared at all about AP rankings. It comes down to the metrics which favour the P5 schools. Is there a bias for P5 schools. Yes the metrics make it easier for them. But within the P5. I would say no. If anything the last time a big blue got really badly seeded it was Kentucky being underseeded in 2014. There is enough data now to separate teams that you don't need to look at AP rankings for example.
Now are the seeds right? They do generally, with some exceptions, select them in line with metrics. But the metrics are so biased by how a conference does before the end of December, that you might not get the teams or conferences that area playing the best. But really what alternative do they have? By January conferences only play each other, so you can't say which one is actually playing best in February for example when they only play each other.
#2. St. Mary's is one of those teams that is hard to compare. The metrics really favour the P5 schools. St. Mary's simply does not have a chance to do welll in Quad One Wins. But it was raised last year, I think by Poppy Hart, do they deserve the benefit of the doubt. A school like Gonzaga does everything it can to play a good schedule, and St. Mary;s I do not think so.
Ultimately you can compare P5 teams by the numbers. But comparing Syracuse to St. Mary's... its apples and oranges. But when you get to teams like St. Mary's it really is the eye test, "rep", and I suspect they consider power ratings.
I will say that small schools are not selected on RPI. For example if Buffalo has a mid 30's RPI, but loses the MAC, they are not going to get an at-large. Not ranked, no rep, and their power rankings are not that good.