I don't think it's very understandable. Not different from any situation where families have different rules for their kids.
Except if schools are maliciously inserting themselves as a party apart from the parents. Which would outrageous and common.
You're overlooking the bullying aspect. The threat is not that they kick out your kid, the threat is that the administration and/or teachers label your kid (and you). From then on, everything that goes wrong is because you as the parent prioritized vacations over school. Stuff like, "How do you expect the boy to think about gemara after what he's seen on a beach in Miami?", and "If they cared about the kid succeeding academically they would only take vacation when school is out" - both of which (and more) I've heard repeatedly (not to mention all the snide comments about how much someone who can afford vacations should be giving to teachers in tips, to the school in journal ads, etc etc). I admit, these stupid reactions are going to be limited to just the bitter, jealous, sad people, but such people exist. And it's very emotionally damaging to kids to be written off in their teacher's mind even if they can pull through academically in spite of that.
You are indeed a paying customer, but they are monopolists, so who really has the power in that relationship? Sure you might have other choices if you happen to live in one of a few communities, but how many of those choices in your area actually offer the same product (hashkafa, academics, etc)? They've got you over a barrel, its not the other way around.