If my understanding is correct then I'm a bit confuse with the example you give on OP.
Wager 10btc on sports at Stake and player will get 0.04xx rakeback (0.42%) while affiliate commission on Stake is 0.30% only.
If I understand it correctly, you get 0.30% affiliate commission but you give 0.42% for the rakeback.
How can you pay higher percentage than what you earn from the affiliate commission?
edit: correct me if I'm wrong
In the case of stake before my website I already being affiliate with them and Eddie increased once my commission for sports to 0.6% and casino to 0 2%. And it might in tease if I get more better results.
Hope also this screen shot answers your question :
https://imgur.com/DR94CWN