I think it depends on the kinds of places you regularly book at.
When I read your first sentence I thought "that is the exact opposite of my experience". Then when I read your second sentence I realize we're probably not using 3rd parties the same way.
I primarily book 4 star and up properties, that is just how I prefer to travel. For those kinds of places you'll often get a worse net experience when booking through a 3rd party (I've tried in the past). Upon check-in, it is made clear that your "discounted rate" doesn't qualify you for certain perks (loyalty points, check-in bonus like a free drink, etc.). I'm also not too worried about a name-brand property screwing me over.
But for a little "seaside hotel" kind of place, I can see where having a large 3rd party booking agent on your side could be valuable.
Booking has stood by me before whereas the little seaside hotel barely has a working phone much less a computer with a person that can operate it.
I have no doubt Booking is fully liable here but for the vast majority of interactions they reduce friction.