Hi Jerotas,
out of curiosity I tried the preset.
Man, that’s a lot of gain.
Not my kind of thing at all, but that’s subjective.
With the Output knob at minimum (“whisper”), there’s no squeal, with either single coils or humbuckers. When turning up Out, it begins.
Now, I don’t hear only loads-and-loads of gain but a lot of noise too. I know that kind of noise, it is emphasis of too much high end combined with gain. The source is High Cut in the drive block. You’ve increased it from 1500 to 20k, as Mr Fender already noted.
Now I read that you’re not going to change that because “I don't like to narrow the frequency range of my expensive awesome pickups so I always leave the high pass and low pass at "non-existent" on drive blocks, and I'm not going to change that”.
Frankly, that’s like sticking your head in the sand. And it’s not true either. Every component in the chain affects your tone and the range of your pickups. The amp itself sometimes narrows the range. The Cabs do. And so on. All those metal players who were or are using Tube screamers in front of real amps, were high-cutting at 800Hz.
And it doesn’t affect tone that much either. Just try it: bring back High Cut to 1500 (default for TS Mod). The tone will hardly change, the noise decreases and the squeal is gone (at the volume level at which I tested). If you really miss some high end, bring it back after the amp with the GEQ.
I would not use the rear input because you’d circumventing the issue. And you may end up with even more noise because the front input has better noise protection.
Also, I’d not call this a bug. There’s limit to everything, even digital. Digital reproduction doesn’t mean that everything is fixable, or everything is possible. The Axe-Fx consists of modeled electronic circuits. There are still laws of nature in effect.
BTW, your mixer suppresses row 3, which has Cab 2 in it. Why is that?