Resource is the least of the problem and definitely the one thing that dev definitely has. I'll show you how the dev could do all that you mentioned. Think about it as if the game will now have 5 different endings instead of 4 because of the harem ending.
Endings 1/2/3/4 are basically achieved by only romancing one love interest in the playthrough. We can agree on this. Ending 5 (harem) is basically achieved by choosing to romance every love interest in the playthrough. So how do we make it work without having to rewrite the whole game? It's reasonably simple. Develop the game without locking the options. Don't create choices where you have to choose one or the other (ex: it's Saturday night, don't force players to choose going on a date with Emma or Lucy), but instead separate them so they don't affect one another (ex: the date with Emma is on Saturday night, the date with Lucy is on a Sunday night) to ensure that each romance route is independent.
Therefore, all 5 endings would have the same playthrough up to right before the actual ending where it branches into ending 1/2/3/4/5. Ending 1/2/3/4 will be straight forward to the end. Ending 5 would be bigger ending because it'd require additional scenes to develop the characters further to fit into the harem ending. Ultimately, everyone would feel pissed off at the start (especially Charlotte and Suzi), but they'd come to accept that MC is such an amazing person that it's best that MC loves all of them equally, and they all equally love him back.
First, this has absolutely nothing to do with what I mentioned, it is a comment on structure from a game tree point of view.
Second, this is a TERRIBLE IDEA in my opinion. What you are saying is precisely that interaction between each route is irrelevant. That makes for very less interesting stories. "Fuck Emma, got her pregnant", no consequences with the mother. Fuck Emma and Sucy, no problem. Treat Charlotte as the best woman in the world, no problem with Lucy.
First you would need to justify why no one knows. I could understand keeping it secret (find it hot when it is forbidden) for Emma and maybe Suzy, but eventually why Charlotte? Nice guy, loves my daughters as a father, they love him back (not romantically in her head) why hide it?
In some sense, precisely what you are saying is that there is no real choice. While choosing to fuck a 18 years old that you were supposed to keep safe should have heavy consequences!
In fact, this approach is what Where the heart is have done, and while fun, in the last update three girls for example realize you have been fucking them 3 (3 friends) and no a single one had any problem? really? That is in my opinion bad writing.
Logically, the justification for Charlotte's character is something like "MC is the only man that I can trust. He is the only one that doesn't just abuse women. I can't trust other men, but I can trust MC. So why wouldn't I trust him with my sister and daughters? I know he'd treat them right". Similarly with Suzi, "I'm overprotective of Emma, but eventually she will find a boyfriend. Isn't it better that her boyfriend is someone like MC rather than Zack or the other useless school kids? At least I know for sure he'd never hurt her".
This is precisely the kind of terrible "porn logic" that happens in terrible games as WMV. "MC is a gift from god so he should be shared", although in a smaller, more family centric scale.
Imagine if every mother would go and say "I love this man, he is the best and he clearly love my children.. yes, he should fuck them" Do you see that realistic?
I also disagree with your notion that Emma is self-centered that she won't share. She literally already wished MC is her dad which implied that she'd be happy if Charlotte ends up with MC. It's only a matter of development that she'd then realized that she also had romantic feelings toward MC, and that she loves them all that she'd be fine with sharing.
Look, nobody loves Emma as much as me, that anyone can tell. But if you think she is not self centered, we must really agree to disagree. She literally received a letter and assumed it was from Zak. She saw Zak fuck another girl and justified it by "she manipulated him, he clearly loves me".
I agree with Emma now thinking MC and her mother would be a great couple. But I think this is good for a different reason. If you go with Charlotte, she will remain a daughter character. If you with Emma, she will eventually start feeling jealous of her mother.
Lucy is easiest to fit into harem, she'd do anything just to be with MC, sharing him with her supermodel sister doesn't mean she's the second choice, it actually means that she's on the same level as Charlotte.
That is not the way an inferiority complex like her would work at all in my opinion! Her mind would go "I fall in love with a guy and of course I have to share it with Queen Charlotte. Not even in love I can be nothing more than Charlotte's shadow." While she might accept it, it would imply she is significantly unhappy.
Don't get me wrong. I'm not asking for a harem ending. I don't think harem is needed in this game. Just want to say that it's perfectly possible to make the character consistent while having harem ending if that's what the dev wants to.
Yes of course, I understand that you don't like it. We just disagree on what is "consistent behavior". But that is fine, neither is the writer here, and if one was the writer, the other would be the critique. All is good.