The two 45's are much better then using an offset flange.
I wouldn't worry too much about the height. Do what you can, and the rest is taken care of by wax.
The Aquia has a 2" flush valve. It isn't going to make that much difference on the cross. The toilets with a 3" flush valve are more of an issue. They flush with enough force to skip across the cross fittings and up the other side.