Ath does not act as a modifier, it's a standalone category. It does effect things like defense, ability to rebound and score in traffic, block shots, etc. like it would in real life. It wouldn't effect things like bh, pa, ft shooting, etc.
And yes, all else being equal, a player with 90 reb and high ath will rebound better than a guy with 90 reb and low or avg ath. But the difference isn't huge, and guys with high reb and low ath can rebound just fine. A high reb, low ath guy will beat up a low reb, high ath guy on the boards.