That's right. If the Matrix is designed to over or under emphasize certain guitar-specific frequencies, then using it would take up some learning curve slack for a new user.
Using a "biased" FRFR solution with the Axe causes a host of other problems though:
~You will never hear what the Axe is actually putting out. All of your patches will be tailored to your biased speaker. Go direct in a decent quality studio and your patches aren't going to sound the way you expect. Send a direct signal to FOH and your patches, which are already compensating for your biased speaker, are going to have to be readjusted in even weirder ways to compensate for the inevitable bias of the house system.
~Having a weird guitar-specific EQ bias built into your FRFR solution is going to cause some of the same problems that guitar speaker cabinets cause; the rig will sound great in some rooms and awful in others. Sort of defeats a huge part of going FRFR in the first place.
~Many users like to match their favorite "real" amps in the Axe through use of varying amp models and different IRs. Using the CLR gives the cleanest artistic "canvas" possible for re-creating the nuances of your real amps and guitar speakers. An overly biased FRFR solution will make attaining highly detailed versions of certain "real" amp/cabinet combinations very difficult.
Some thoughts:
Many of us that use FRFR speakers want our rigs to only exist in the Axe. That, for me, is the whole reason I got into modeling in the first place. I don't want my sound reproduction solution doing ANY of the coloring. That means I have to learn the Axe well enough to be able to dial in what I want to hear. The Axe is not a plug and play toy.
If your Axe patch or patches sound bottom heavy and/or "boomy" through the CLR, then you have dialed in bottom heavy and/or "boomy" settings in the Axe. You can buy FRFR solutions that sound different than the CLR, but you cannot buy any FRFR solution that is more accurate and transparent at giving you exactly what the Axe is sending; i.e. you are hearing the full capability of the Axe reflected through your settings and choice of amp model and IR.
If your Axe patch or patches sound bottom heavy and/or "boomy" through the CLR but they sound "not-boomy" or bass heavy through your other FRFR solution, then your other FRFR solution is not accurate or transparent. That's just the way of things. There are insurmountable physics issues involved that transcend your and my emotions and opinions. <---This is a tough one for lots of guitar oriented folks. As soon as FRFR thinking is engaged, guitar speaker thinking must be dis-engaged. It is very difficult for guitarists to shake the thinking that says, "my speaker exists as part of the tone shaping process".
With the CLR, your choice of speaker IR is arguably the most important decision in the creation of your patches. Ignore the names of the IRs and experiment. I originally used only the near field IRs that come with the Axe. Jay convinced me to relearn the Axe using only far field IRs. That made all the difference in the world for me.
If I needed biased speakers to "color", "warm", or in any other way shape what is coming out of the Axe, then I wouldn't want to use the Axe. That was the way things were back when the first modelers came out. Those days are long gone. But the price tag for full investment in the "it's-all-in-the-Axe" modeling paradigm is surrender of guitar-speaker-mindset.
The CLR finally gives the live Axe user a truly transparent live sound reproduction system to create with. What you dial into the Axe is what will come out. The CLR will do nothing for you. It will not add. It will not take away. All the tone work has to be done in the Axe.
