I'm trying to picture why it isn't flat... Did you replace the original flange with one made for the 320 or are you re-using the original flange? I know Dometic makes an adapter to use with the 320 for 4-bolt flanges.
As an aside, we decided to jettison our Aria electric toilet also, but I took the easy way out by going with the Aria manual flush version. It was crazy expensive, but that way I didn't have to change any of the mounting hardware and the toilet fit exactly the same over the hole in the floor tile.
2003 Country Coach Allure First Avenue 36; 2012 Honda CR-V