I have a Low cut of 101 Hz in the cab block already. im starting to think it was just the new speakers we used for our PA. When Ive used this preset live my only issues have been level volume across scenes. But now that you mention this preset isnt set to sit in a band mix at all makes me wonder because sometimes the Herbert scene that I dont have boosted is a bit harder to hear through my in ears and I wonder if thats because of all the low end. But Im pretty sure it sounds fine FOH. I could maybe try a new cab but I know that will drastically change the sound which I dont want because I really dig the soundDevs preset isn't really set up to sit in a band mix at all. With the Cali cab (which isn't the IR he uses) the bottom end is completely overbearing. You'll need to apply a low cut in the cab block if you really want it to sit well with a bass player. There's no real way to keep all that low end unless you convince the bassist to give up that frequency range... good luck! lol.
From my tinkering with his preset, I found 80hz-100hz to be the sweet spot in still keeping the low end punchy without creating a wall of flub when you bring a bass into the mix. You will likely find your sweet spot is different depending on your guitar/pickups etc.
Devin also runs his FX in parallel so he can control the level of the FX without it stepping all over the dry sound. His FM3/AxeFx3 preset has them in series. So the moment you engage the reverb you start bringing in a lot of excess bottom end that's harder to control without changing the character of the Herbert "crunch" too much.
I'd recommend trying a side chain and put all the FX after the amp there and either control the levels of it with a volume block at the end of the chain before returning to the output, or just running it to a separate output and controlling it at the mixing board. Should give you a little more flexibility with taming the fx making the low end blossom outta control without having your main crunch from the Herbert drastically tweaked.
Establishing what balance works best is something you and your bassist should do at rehearsal. You may find you both need to make tweaks that may not sound terribly appealing on their own individually but together work very well. Basically, let the bassist hold down the low end. Don't be afraid to give up some of that boomy bottom end that sounds good isolated by itself in exchange for a better all around mix as a band.
Edit: Just noticed the different settings in the Cab preamp block. Should I lower the bass there and apply low cut there as well?