You have to remember what the mindset was going into poe2.
They saw the success of poe1 but saw how far it had strayed from their goal of a grindy difficult punishing but also rewarding experience. PoE1 became a game where unless your build was 1 tapping entire screens moving at > +100% MS, many didn't want to even consider it viable, and certainly not popular. 99% of the content there is trivial with a bit of practice.
They went into poe2 wanting to make a far more grueling and challenging experience that forced players to stay on the edge of their seat at all times requiring constant focus. Flask usage was part of that. They like flasks, but only when you as the player actually use them. They wanted to all but kill any form of automation (though oddly left in one of the single best sources of automation in the entire game w/ CoC). With flasks having to be used manually, they wanted to provide ways for you to improve it like any of your other metrics like life (oops, nm), defenses, damage, etc. They had figured all players would of course need to be constantly monitoring flask usage and would want improvements for it.
When 1.0 officially launches and a whole new wave of players who haven't played poe1 and don't want to pay for EA come in, maybe they'll finally get the undeniable feedback that literally no one wants this and give up some of their absurd design philosophies.