I visited Uluru and Longitude 131 five years ago and the OP's thoughts echo my own experience. Although I stayed at a less-expensive option a couple miles away (Sails in the Desert?), every concession in the area was managed by the same company. If you want to see Uluru, you have to sign on to ridiculously overpriced lodging, even at the campground. Because the prime experience is observing Uluru at dawn or dusk (yes, fairly spectacular), you basically have no other option than to overnight.
I did tour Longitude 131 and had lunch there -- it struck me as tasteful and pleasant enough, but nothing special as far as boutique hotels in the wilderness go. When I heard the nightly room rate, I was agape. It is extortionate.
As far as this being a remote location that is expensive to operate, that's true to an extent. But the airport is served by a couple Qantas jets daily, and there is highway access, so supplies can be trucked in. And it's a big operation -- there are hundreds of hotel rooms, not just this one resort. (My guess is that the biggest challenge is staffing, because the location might get old pretty quickly.)
I've stayed in several safari lodges on two trips to Africa that were priced upwards of $1000/night. A couple of these had no paved road access and some provisions had to be flown in by small plane landing on a dirt runway. The challenges of running one of these operations would be infinitely more difficult than those of Uluru. While accommodations were somewhat more rustic than the spin-and-span Longitude 131, these safari lodges were more interesting, unique, memorable, and personable, and the value for money seemed surprisingly fair.
See Uluru, but keep your lodging expenses to a minimum and spend the savings on a more worthwhile splurge elsewhere.