Yeah, I stay at places that you can't book direct so infrequently, that the "rewards" with the 3rd party site don't really matter because I'll never get enough points or nights to redeem them. So I go with lowest out-of-pocket. I'm not sure it would ever be worth it to pay more now for a possible future reward (unless your trip is long or you travel so predictably that you can calculate the actual benefit of stay 10 nights get one free, for example).
Just yesterday I just booked on Expedia for a hotel that only uses 3rd party sites. All the sites show the same price, free cancellation, no extra fees. Expedia said I got 10% off by reserving while signed in to my account - it was the best deal I could find, so I booked there. Since it's free cancellation, I'll still keep checking in case there is a sale somewhere else. The last time I had a non-direct booking (that wasn't free through a credit card reward site) was at least 4 years ago, so any rewards from that stay are long gone.