That playing bot games can inflate your rating means there is a fundamental problem with the rating system, it's not doing its job correctly.
Okay, so I have gone back and forth, up and down on this, because I agree this is a troubling result. I also peeked into some of the recent stuff on chess ratings, which have had a surprisingly checkered and complicated history (I thought things were weird enough decades back when I was still playing "competitive" chess). At the very end of the day, I think the root of the issue is ultimately the one raised by Polk5440:
Also, Trueskill is designed to be very good when players of similar rankings play each other (which is why microsoft paired it with an automatch system for its games). Trueskill will be bad if players don't sufficiently mix. There aren't "enough" comparisons made and comparisons between sets of players who don't play each other become much less reliable.
I think what was really going on here was that we had was a mixture of two subpopulations of "Pro" Dominion players. One subpopulation played a really low proportion of games against bots. Another subpopulation, rich in novices, played a pretty high proportion of games against bots, and humans who played a lot of bots. Most of the novices who play bots are, not to be too judgmental, really poor players. And there are a lot of them, and, in aggregate, their role in this story is to "feed" points to the bots.
A relatively small number of players playing mostly bots and players who played bots were of somewhat higher skill, so were in turn "fed" some of the points the bots ate. Back before the "Play Bots" rating system switch, this wasn't a major problem in Pro land. But after the "Play Bots" button defaulted to Pro, there really was a big inflow of points to bots from novices now suddenly playing in "Pro" land, which were in turn "fed" to the mediocre players (including me).
Problem: this population of middling players don't mix nearly as much as you might think with stronger human players, so "The points stopped here". Without the kind of mixing Polk5440 mentions, two players that have (say) a 5000 rating could be very different in skill if one player's rating was padded by bots and the other player's wasn't. The good news, is that I think we can (and just have) "drained" the bots points out of the system, but there is still a fair amount of disconnection or lack of mixing in the system, and my hunch is that when/if there is some correction for that, there may be some downward ratings pressure on at least a subset of the (say) Top 500 or so as they lose the same proportion of games as previously to the bot-inflated players, who now have lower ratings.
In any case, it's an empirical question.