Well, the rain has just let up so I went out to have a careful look at the car.
The mechanism has definitely been replaced as the new one looks different to the old version. On pressing the release button, the flap does open but only slightly. You have to pull it open with your finger but it does seem to work like this every time. The new design still relies on the flap moulding sliding into the car housing to align the flap and this is still a little tight although a lot better than before. I think a little bit of Vaseline will help when everything dries off. The spring force opening the flap seems a lot more than previously.
Regarding the trim removal, they clearly did something in the boot as my tray (non Lexus item) was moved. They told me that the rear seat area had been removed but this looks fine and there are no rattles so far. They didn't vacuum the rear footwells after they had been in the car but this is not a big deal.
So, OK thus far.
BTW AJ, have you seen this previous thread: