On most of our recent rentals, we have had similar experiences:
When we pick up the car, we go over it obsessively and obviously, in the presence of their staff. We note every slight hint of a scratch or suspected potential scratch, wrinkle, smashed bug, bit of dirt, etc, and take LOTS photos, all while their staff members stands there watching us, as he repeatedly marks e-v-e-r-y little glitch we note on the paperwork. After a few minutes of this, the guy typically stops checking each thing we point to, he just scribbles another mark on the car diagram when I point, probably rolling his eyes. We go round the car with a super-bright flashlight, camera, taking our own notes. At the end, the guy hands me my copy of the pre-trip inspection report, and the car is absolutely covered with little scribble marks - there are virtually no places on the car that are not marked with some sort of scribble. I'm handed the paperwork, the guy gives me a strange look, which I interpret to mean "look, every inch of the car shows a scratch, we're not going to hold you responsible for any you add, unless a large piece of the car is completely missing."
Last car I returned (at the airport in Malta, about a week ago), they didn't even bother "inspecting" the car; the guy just looked at the paperwork, told me as I handed him the keys "your deposit has been released from your credit card, have a nice flight."
Works for me.