This is all true, and it also touches on an even bigger problem that I personally have with meaningful choices when it comes to harems and choosing girls, and that's the limitations it puts on your writing: the main one being that it means the girls themselves can't be used to drive each other's stories and character development forward.
To give an example, the entire subtext behind Vicky's sudden, seemingly out-of-nowhere attraction to the MC early in the story is her hidden inferiority complex comparing herself to Lucy, who the MC dotes on much more than he does Vicky. It's never explicitly articulated, but there are a tonne of obvious clues pointing towards it. None of that makes any sense, however, in a world where the player has the opportunity to reject Lucy. In fact, the player rejecting Lucy and pursuing Vicky alone would completely change the dynamic in their early relationship; suddenly, the MC is chasing her just like every other guy does (something she's more than used to) rather than rejecting her for the shy loner girl (something that's alien to her).
Now, obviously, you could write all the individual scenes a dozen different ways to account for this, but at that point you would be fundamentally changing all of the subtle story elements that drive the girls' character development, meaning that the characters themselves would have to be changed, too. To put it another way, different story input = different character output. That quickly becomes an impossible task to do well, you'd essentially have to write dozens of different stories all at once. So, instead, what I think tends to end up happening most of the time when devs do this is that in order to reduce the impact of player choices, the girls end up siloed off into individual stories of their own, where they are deliberately designed to have minimal impact on one another. This, in turn, leads to the standard template where the story has 90% of its run time devoted to the MC following simultaneous individual girl paths, perhaps with the occasional crossover and carefully worded group scenes that are so generic they can fit every path, but with the harem itself, the bit we're all here for, being relegated to an ending, not forming the core of the story.
Hmm, that turned into a bit of a ramble, but it's something I've thought about a fair bit over the years and I just kinda vomited my thoughts out!