I guess amenity fees are basically a way for hotels to reduce the qualifying spend and increase the non-qualifying spend so they need to pay less to the loyalty program. By now I assume it's also become a competitive necessity in US locations where other hotels also have amenity fees, given that price comparisons are listed without taxes and fee in the US.
I recently spent a couple of days at a Holiday Inn in a "resort location" with free parking listed as an amenity when booking at the IHG website. It also says on the hotel website that parking is complimentary for hotel guests.
However, I had to pay an amenity on top of the qualifying rate and guess what that covered: parking, in room safe, local phone calls, business center access, fitness center and a local shuttle. Things that would be included in the rate at most hotels in other locations.
To be fair though, the amenity fee was waived for one night that I paid on points at this location. It seems to be very much up to the individual hotel policies, whether the fees are waived for reward nights at IHG hotels, because I've both experienced being charge and having it waived.