Well... I never used a Boss MT-2, and have not played with the Fractal model of it. Was a long term Boss HM-2 user when they first came out (seriously, I am that old), but while I still have an HM-2 in one of the many boxes of assorted effects pedals, I haven't used it in a long, long time. It didn't have a mid control that I remember, so mids were scooped by turning treble and bass up, and level down. So take all of this with a pinch of salt and let your ears do the guiding.
There is no normal! The article you have linked to is interesting, but is really talking about using an MT-2 to achieve a more recent sounding tone than most people bought the pedal for back in their heyday. A bit more punk/indie than classic hair metal and the heavy tones that followed. All a matter of taste and what you are trying to achieve, but they are setting it up a little like a Tube Screamer in terms of tone.
Your distortion setting is probably in the ball park - I'd maybe try a little lower (maybe 3-4), but we still need to talk about level and gain. Bass setting on the low side now that you have set a low cut in the cab block. You should be able to bring the bottom end up without letting too much "mud/flub" through. Because you are boosting the mid, try increasing the frequency a little. It will make the guitar more audible in a mix with other instruments, but can make it sound a little honky. 500-600Hz generally sounds good to me for boosted mids, 700Hz can get honky. 370Hz is quite a good frequency area to cut some mids, but for mid-boosting I tend to go for slightly higher frequencies. You treble setting is higher than I would use, so I would normally bypass the MT-2 and see what the amp sounds like on its own. If it can take a bit more treble and/or presence, turn those up on the amp, and then re-engage the MT-2 and take the treble on that one down to suit. It will likely make things less fizzy sounding.
So, effect level and amp input gain. You don't mention what level you are using for the MT-2? You need to make this work in combination with the amp input gain. Here is how I generally do it:
Bypass the MT-2 and set the amp for an input gain setting you can live with. For most that means somewhere between highest end of clean, or a little way into crunch tone. Once you are happy with that, turn the MT-2 back on and adjust its level so that you get a slight volume increase when you switch it in. From there you can go on to adjust how hard the pedal pushes the amp, because increasing the output level of the pedal will do much the same as increasing the input gain of the amp. With physical amps and pedals most of us are kind of stuck with setting the amp input gain for a good rhythm sound, and then a bit stuck with how much extra amp drive can be added when the pedal is switched in, because it gets too much louder than the rhythm sound. Of course with the Axe FX no such issues are insurmountable, because we can just make a rhythm Scene with the pedal bypassed, and a lead Scene with the pedal engaged, and then use per-Scene level controls to make sure they are both at appropriate volumes. I still find this mind-blowing, but I'm a simple soul!
Hope that's enough to keep you away from mid scooping the output EQ. It's cheating in my mind too, mostly because you lose all the glory of a tube pre-amp's subtleties in dealing with the frequencies delivered to it by the pedal. Seems a waste of Fractal Audio's detailed modelling just to trim any EQ issues at the output, when they could be part of the fully modelled tone.
Liam
) about the importance of mid frequencies. Turn the mid control right down to get a very tight and "mid-scooped" sound with anything that offers that control. You can build body, fullness and listener fatigue/annoyance by turning the mids up. It's essentially the "obnoxious" control that Frank Zappa maybe dreamt of.