The former is one of those Acceptable Breaks From Reality (specifically see Arbitrary Headcount Limit) you just have to deal with in RPGs. If that could happen, every battle encounter would have to be balanced around the fact that you have to lose your ENTIRE party to have any possibility of failure, so enemies would have to be so much stronger that losing characters would have to become a normal thing (or else just write off the combat as a speedbump), which I personally would find annoying. As for the latter, that's a matter of the game's systems- I think Final Fantasy X was the first game to allow this (or at least the first really notable one) and it was considered a major innovative feature of the combat system. I don't even know if RPGmaker allows it.
in the harem game you can switch party members during combat so at least the rph maker engine allows that, you still get a game over screen if the front line dies so not if that can be changed