I actually just noticed this, I did notice it happened maybe 1 in 5 games when you have all acts checked + prioritize bonus act checked and didn't think much of it. However I am currently running bounties with bonus checked and A5 UNCHECKED. But no matter what game it makes, or what act is the bonus. It never does it first, It selects the act randomly it appears. I have had it select the bonus act properly maybe a few times out of 20. The main issue like you said, because its not doing the bonus act the bot is then completing single 4pc mat bounties whereas it could be doing them in order to get bonus caches.
I understand if say, Act 1 was bonus, it completed it then next A5 was the bonus and my bot has A5 unchecked to SKIP it, that it either leaves the game or keeps going on non-bonus. But its not even working like that. I might make a full thread regarding this, maybe its just a minor bug Taras can fix or if its somehow working as intended when you uncheck a act but keep priority checked.