Yup, and having needed customer service the one time I booked a flight through booking.com, I can confirm that they absolutely get in the way - a name change on a ticket turned into an almighty rigamarole with charges left right and centre - even though it was booking who had truncated the name - and the airline wouldn’t talk to me directly as I wasn’t the booking party, booking.com was. The airline said the change would have been free if they could do it themselves, but the request had to originate from booking.com, who not only charged nearly €200 but also took so long about it (a week) they were almost too late.
I never thought I’d find myself arguing Ryanair’s corner, but adding booking.com to the mix likely just makes an already poor experience with Ryanair truly dire.