OK, that makes sense.
I was just playing with a similar idea trying to delay the D.I. guitar to see what the effect would be. But, at least in my experience, MG3 is processing audio-to-MIDI conversions so fast that I’m not hearing/feeling any real issues in terms of perceivable lag on the synth side. Has this proven to be a significant issue for you already?
So, this has been a bit confusing for me too. I’ll try to explain how I understand it and @JamO can correct me if I’m wrong.
You can allocate eight audio inputs to MG3 in standalone or any of the plugins.
BUT: In standard mode (non-hex), MG3 listens to Ch. 1/2 only. In hex mode, MG3 listens to Ch. 3-8 (w selectable option for D.I.: Ch. 3-8, Ch. 1 only or Ch. 2 only).
When in regular tracker mode, if all eight channels are connected you will see a message: “TOO MANY INPUT CHANNLES. TRACKING QUALITY DEGRADED.” …but MG3 is only going to use Ch. 1/2.
If you allocate your QC to MG3 Ch. 1/2 (while in hex tracker mode) MG3 will default to using the aggregated hex signal from Ch. 3-8 of your GM-800, unless you choose either Ch.1 or Ch. 2 under CONFIG.
I verified this by feeding the processed outs of my Axe-Fx II to MG3’s Ch. 1/2. In hex tracker mode, the processed audio is inaudible, yet there is definitely a clean D.I. signal available on any chain. Therefore, MG3 must be aggregating the hex signal. EDIT: This is only partially correct. You can still select Ch. 1 or Ch. 2. as an input source for the chains (under CONFIG).
When the MG3 plugin is hosted, you can basically route anything you want to Ch. 1/2. Where the host allows, this is eay to configure. But, again, it will only be used as a source in regular tracker mode.
But, using MG3 in standalone with an aggregate audio device, one issue is that there is a limitation on configuring the input source for Ch. 1/2 when the channels do not follow a specific order, i.e. Ch. 1/2 must fall in sequence before your hex channels that feed Ch. 3-8.
Like you, I also use an aggregate audio device. I tried to feed the D.I. channels from my Axe-Fx II into Ch. 1/2 of MG3 and the SY-1000’s hex Ch. 3-8 into the respective channels of MG3. As the Axe-Fx is the final device in the aggregate, the channels cannot be lined up. However, you can acheive this routing in a host without issue. Just the actual input source will be dependant on the selected tracker.
Does that make sense? I hope so 
FWIW, I did find a way to acheive what you want but it’s a little convoluted. I had to use Blue Cat Audio’s Connector plugin to grab and send the D.I. signal as network audio from the Axe-Fx II D.I. to another instance of BC Connector asting as as a receiver positioned in front of the Cory Wong X plugin in MG3. It works perfectly, but it’s a lot of work to get a specific D.I. signal. Makes more sense just to get a D.I. from the SY-1000, in my case.
It seems to me that MG3 might be able to do what you want it to do if there were: 1. a more rigourous method of allocating the input sources of Ch. 1-8 in MG3; and 2. some allowance made regarding how each chain in MG3 chooses its input source, i.e. maybe you would have a module that you need to select to get hex input on any given chain.
I’m a little on the fence with this. It seems easier to just route it all in your host/DAW. But, it would also be cool to be able to use MG3 as a one-stop host for all your audio processing needs.