It's interesting that the resellers/brokers wouldn't have figured out a way to conceal the booking source. Like obviously the hotel knows if it didn't come through them, but Expedia is far from the only bulk-inventory broker: travel agents, airlines, credit card rewards programmes, etc are all basically doing the same thing.

My work travel is typically booked through perk.com and I don't get the sense that I'm treated resentfully at any of those properties.