My parents and my Aunt checked out of Wilderness Lodge yesterday. They are local and made a last minute reservation after the parking fee went into effect. They knew about the fee beforehand because of me. They were not informed of it by the phone CM until after the deposit was made, just like when you book online.
When they arrived at WL via their car, told the Guard they were checking in, the Guard scanned my Dad's Magic Band and waved them through with no mention of the parking fee. They had not gotten their room number texted yet and it was around 3, so they went to the Front Desk to check in . Checked in, got their room, etc and no mention of the parking fee. They were not asked if they had a car.
They had an 8 night stay booked and my Dad left after 4 nights. He had a golf trip in Naples with some friends and was gone, with the car, for 3 nights. He came back with the car and stayed the last night.
When they checked out there was a parking fee charged for 5 nights.