I think you're talking about common modifications that the booking website understands how to make via the hotel's API. The GP, meanwhile, is talking about completely arbitrary stuff that is not part of any booking services's data schema for "modifiable properties of a booking"—and also, where the hotel likely doesn't actually
have an API, because it's just some family-run thing, and the booking website is maybe just sending the hotel a fax to book for you.
In the boutique + arbitrary case, what you want is to talk to a real person, explain your issue, and get some kind of free-text note added to your booking in a way that staff will actually follow the instructions in it. You also want this to potentially increase the cost of your stay (rather than your request being denied on the basis that such a modification would increase the cost of your stay.)
If you book through a booking website, and then you speak to the booking agent to make such a modification, they will have no ability to add the note to your booking in the hotel's computer in such a way that the staff will take it seriously; nor even, necessarily, the ability to confirm that that modification is something that the hotel can do for you. (They can call the hotel... but they're just as likely to be brushed off as you are.)
If you book through a booking website, and then you speak to the hotel, they will tell you that they can't help you, because they want to charge you more, but they don't have the ability to charge you anything, since they're not billing you; they're billing the booking agency. And the booking agency itself has no way for a hotel to add an SKU for this kind of customization. (If it did, it'd be abused by unscrupulous hotels.) They'll then tell you that they can fix your problem if they cancel your agency booking and then re-book it through the hotel itself... but in so doing, you might not be able to keep your reservation.
If you book through the hotel, you can just speak with the hotel, and enter into whatever private direct customer-to-business deals you like with them to negotiate whatever kind of special service you want from them.