You're understanding of the 990's behavior is accurate: when mains are set to "small" and analog bypass is enabled, the 990 sends full-range data to the mains but also makes a copy of that data and sends it to the sub.

One thing that might be worth tinkering with is setting the mains to "large" with a crossover set to around 40Hz or 60Hz (depending on which floorstanding Axioms you have) and the sub set to "L/R+Sub". This will cause the 990 to always send full range data to the mains, but when digital bass management is active it will also send a copy of the low frequency data from those channels to the sub. The crossover point would take some tinkering, since you'd probably want to get it low enough for the speakers to be rolling off naturally. This scenario would give you "large" mains, though, which means that the analog bypass mdoe would not involve the sub at all.