It does make sense if you consider that YOLOdice has other costs too, such as rakeback which goes up to 30%. I'm sure they'd rather have investors handle that instead of hoping that players lose to pay rakeback. The alternate system (50% of net profits) also has it's own pros and cons. For example, if a player lost 50 BTC and then won it back, commission would get paid as if that player lost 50 BTC.
I'm fine with the system, it makes sense to me. It can simply be confusing, it was for me at first as I lost a lot during that LTC massacre. It will probably take years to recover from that.