I just got back yesterday. We rented a car and stayed at the Wilderness Lodge (reservation made a few months ago, so well before the Match 21 cut-off).
Of the CMs we encountered that could have/should have mentioned the fees to us, no one did - not at check-in (we did online check-in but ended up having to go to the front desk anyway, as they never texted us our room number) nor at the security posts when entering the other resort lots.
There are not separate lots for overnight and day guests. We really enjoy resort dining, which is a big reason why we rent a car. We had dinner reservations at Animal Kingdom Lodge, the Grand Floridian and the Yacht Club during our stay, as well as a breakfast reservation at the Polynesian. Each time, I (the primary guest on the dinner reservations) had to scan my magic band with security upon entering the parking lots (they wouldn't take my husband's, I think I just had the reservations as "Ariel484 and Guest" instead of "Ariel484 and Mr. Ariel484," so maybe that's why). So I'd scan, they'd tell me where guest parking was and to enjoy our meal. Never mentioned the 3-hour limit, or that I had to bring any kind of a receipt. Every time I approached security I'd say something like "we're here for a dinner reservation" so I'm not sure if they would have just let me in if I said I wanted to park and hang out or whatever.
We were definitely parked at Yacht Club for longer than 3 hours (arrived a couple hours before our reservation to walk around a bit before dinner, then did a little post-dinner stroll). I think we may have also been at the Grand Floridian for longer than 3 hours (Trader Sam's visit before dinner at Citricos).
So "how are they enforcing the three hour restriction"? I have no idea!
And sidenote: we never had trouble finding parking at any of the resorts we drove to. In September we stayed at the Yacht Club and they had some sort of conference going on - they told us to just "make" a parking spot where we could (boy was I not impressed by that!). This time, tons of open spots.
Second sidenote: I got billed for our room charges this morning, but realized I was never emailed an itemized bill. I need to look into that and make sure they didn't actually charge us to park. I also need to do a better job of keeping my own receipts in the future.