When I'm able to, I run "aux fed subs" for one reason only; to keep some microphones totally disconnected from the subs. What I run is more what one would call group fed subs, I send the channels that needs subs to a group, and feed the subs from that group.
Anything that goes to the subs will be as aligned (or not) as the system is, so there are no issues there.
The vocals and other non-sub instruments will go straight to the full range tops, so there is no lack of fullness if that's required.
I do crossover between subs and tops quite high when using "single hang" (no I don't have two line arrays, so most of the time it is single or double tops) mode, this to avoid working the tops hard in the lower register when they are to reproduce vocals.
It seems to work, only problem really is that most mixers I've seen doesn't let the Master fader control the 5-6 channels of separated output streams that my setup produces.