That problem is not really significant currently, because the transaction fees are insignificant, but I'm pretty sure the pool operator will address this when the transaction fees will become significant. It is just difficult to devise a "fair" way of paying the transaction fees to the miners, because contrarily to the block reward, their value is unpredictable and varies a lot.
This will be the big test of Bitcoin. If we get a bunch of halvings, price doesn't increase significantly, and/or transaction fees don't increase, Bitcoin has a problem.
In other words, hang on tight. It'll be a wild ride, and no one knows where it'll end.
M