It sounds like you're going to use the Axe FX pretty much like a pre-amp and not use the power amp or cab sims? If that's the approach you're taking then the difference between the two Mesa amps will be when you've turned the volume up to the point where the 2:50 starts to distort, (which may be a good thing if you're after real tube amp output stage distortion). At that same point, the 2:90 will still have a little headroom left before it starts to impose it's own sonic signature on top of the signal coming from the Axe FX. That would be good if your motive is avoiding the amp making it's own contribution to the sound as much as possible.
My own experience with both a Digitech RP500 and a Line 6 HD500 as preamps with a Carvin TS-100 power amp through various cabs taught me a lot. Running, say, a Fender Bassman model with a 4 x 10 (which both the RP500 and HD500 had) cab simulation into either my Tanoy monitors or a couple of floor wedges using a clean solid state amp, the sound that came out was a fair approximation of an old tweed Bassman. Running it through the Carvin and a couple of Tone Tubby 12" speakers sounded like something else entirely as both the Tone Tubbys and the Carvin added their own sonic signature to the mix, with the sound of EL-34's starting to breakup coming through loud and clear, but only when I cranked the amp. Now some of those "hybrid" sounds were cool, but I thought most of them sounded better if I turned off the speaker sims in both processors and used the pre-amp only simulations in the HD500, while turning off the amp emulation in the RP500. In other words, the louder I turned up the rig, the more it sounded like the Carvin/Tone Tubby combination, and the less it sounded like the Bassman. Guitar amps and speakers are designed to produce sound, not reproduce it. Running amp sim distortion into real amp distortion or speaker sims into real guitar speakers may result in something that's cool sounding and maybe not.
Your cab and amp combination are going to color whatever sound goes into them, for good or bad. This would probably be good if you are running something like a MARSHALL JMP-1 PREAMP on the Axe FX but a little less so if you’re running a Deluxe Reverb or an AC-30 sim on the Fractal and expect the result to sound much like either of those amps.
