I think I didn't make myself very clear. Yes, you are correct, the Genius Booker programme does not affect the RATE of commission that Booking.com charges but it does affect what you actually get. Let's break down my example;

Normal room rate $138.00 - Booking.com Commission (15%) means they get $20.70 - Retrospectively we then get $117.30 for the room ($138.00 - $20.70)
Genius Booker $124.00 - Booking.com Commission (15%) means they get $18.60 - Retrospectively we then get $105.40 for the room ($124.00 - $18.60)
In the above example, Booking.com offering 'Loyalty' guests a discounted room means they only lose $2.10 in commission but we lose $11.90 per room after commissions. Or put it another way, we lose, in total, $32.60 per room due to Booking.com instead of a guest booking direct with us at $138.00 per room - 24% of our rack rate if you like!
Sorry that's long-winded but its the best way I can explain it!
They're offering discounted rooms at our expense!