If I am willing to pay Y for an item, regardless of who is involved in the transaction then it doesn't matter if a percentage is taken. i.e. if Y = Y x 0.97 + Y x 0.03, who cares? Now you might say I could have negotiated that 3% off, and I'd argue that's probably not true.

I seriously lowballed the builder on the sale, the only reason I think I got it was the relationship the builder had with the realtor. The builder has incentive to give a discount to a realtor, as he has 50 other houses he has to sell. She also has an incentive because the quicker she can get me to buy a house, the less she has to show, i.e. the more she makes per hour.

All of this isn't exactly explicit, but in my case, the realtor and I discussed this. It was actually quite refreshing and definitely worked in my benefit as I picked up my house for around 10%+ less than the people around me. The realtor was similarly happy because I only took around a day of her time, and the builder was happy because he was in serious need of cash flow.