yeah something never eluded too or even hinted at, at any point in the game before hand that's why people have a problem with it because it makes absolutely no sense.
Honestly a simple solution to that would have just been to leave it up to the player.
I could see how someone could choose to take it either way. Early on it seemed like the MC was kinda forced into a "relationship" with her but later you were able to choose whether to continue with it or not, you could refuse her. I am not really sure why the player wasn't allowed to decide for themselves if they wanted her in the harem ending or not.
I mean maybe because it might seem out of place that she would go with MC after he took down victor but honestly Mila didn't really come off as wanting to be a part of that life anyways. At least to me.
But yeah, could've simply left it to the player on whether they wanted to accept her feelings or not, rather than forcing a choice.
I for one would have liked to have Mila over some of the other LI's that to me felt more like flings at work. I get Mila could be tied to a life that MC wanted to get away from but also, she could be what helped him through that life and in the "harem" end, he came to realize that.