ioTon is correct. The timing won’t be exactly the same if you send outputs via two different methods (some using physical outputs from a console and some using outputs from the stagebox). The same is true with inputs from different devices (whether a stagebox or console).
I was surprised to measure this myself using Avantis because Allen and Heath’s marketing department does a great job in selling the idea that the consoles are “phase coherent”. But that only applies when you use I/O from the same device – the same console or the same stagebox. As soon as you start mixing and matching I/O sources, the phase coherence goes out the window.
Of course even if the outputs are coming from the same I/O source, the physically placement of the subs vs the mains might result in the signals not being exactly in time as well. So while using two different I/O sources will certainly cause a slight timing issue, it isn’t the only way it occurs.
All this to simply same that using two different output devices will certainly work and no one will “hear” the delay, but it does effect phasing and you can likely get a clearer overall mix if you have the ability to measure the latency between the subs and mains and make corrections on the console (delay setting) so the timing does match. Of course this is best practice in every situation, even when you are not mixing I/O sources.