Personally I find it refreshing since ingame there is just no way of knowing whether or not there will be consequences same as in real life - it's a gamble.
With all due respect, none of this is true at all. Not even in the slightest. The game tells you outright that there are consequences. The first time you use a tadpole, the narrator says you feel yourself lose something you will never get back. There are multiple instances of this. The tadpole menu itself shows the advancing destruction of your brain. Saying it's pragmatic also makes no sense given that menus. It's not about it being evil, it's about it literally destroying your brain. Not transforming != getting your brain back. It's like having a real time simulation of your lungs and saying smoking is the 'pragmatic' choice when you can get by just fine without it. The problem is that what the game says will happen and what actually happens are at odds.
Better endings? Why? It's highly debatable and even less provabale you get a better ending by being a good person IRL - so why should THIS game be any different, it's a moral and philosophical decision which I find highly refreshing, just because we're used to cliches in games/movies/books certainly doesn't mean they should be followed or that a game would be better for it.
TLDR: a hard NO
As far as better endings go, you might have a point in any game but this one. You know, the game that already decided that evil playthroughs get punished IRL with less content and already makes good playthroughs superior objectively and has very few nuanced choices in its writing is the last place I would look for any kind of moral subversions.
