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.
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.
I once mentioned that while checking in at a family owned hotel, and they said they appreciate that the booking service allowed them to compete with larger chains on that front.
Perhaps if there was some "shopify of accomodation" it would be easier to have a seamless experience. In the meanwhile, the existence of a stable reference point gives the false sense of a trusted travel assistant.
I take advantage of their platform moreso than they me. I book refundable no-pre pay hotels every time, sometimes having multiple bookings for the same week. It's like a free option on future pricing.