For sure. I've owned real 800s (Still have a 2204), Mark Boogies (Have a IIC+ in the studio, bought and sold a Mark I and IV a long time ago) etc. and the Axe FX really does do both amps justice.
For Mark Series, in my opinion, the Bass/Mid/Treble knobs really don't EQ in the traditional way as most guitar amps. They really affect the feel and slightly shape the tone. Cranking the Bass knob on a Mark IV (Real or axe fx) just loosens or tightens up the low end. It doesn't really ADD any bass. Use the Graphic Eq to add the low end. Same with the mid and the treble knob. They just shape the tone slightly by either making the tone brittle (Treble knob) or adjusting the smoothness/Honkiness (Mid knob). Again, the graphic EQ is what really adds bass/mid/treble. Hence, cranking the mid knob to 10 isn't going to really add that much midrange, but rather, just adjust the honkiness/smoothness of the overall tone.
As for the JCM800. It's not my favorite amp in the world, but I was using it as an example of what to listen for when you're trying to get your guitar tone to "cut" live. Just listen for where your guitar sits when you're using the JCM800 amp block. Dial your ears for that. Then, switch to your favorite amp and cab IR and listen for that brash upper-mid thing and try to get your tone to do that. What sounds bright by itself, will sound perfect in the mix.
I personally use the Plexis, Bogner Shiva and the AC30s for my rock rhythm guitar tones, depending on the type i'm going for.
Edit: The Bogner shiva is dark by nature. I crank the mid and the treble to brighten it up and use the bright switch and switch to EL34 tubes. I just like the way the amp feels because it is a lot looser and squishier than the average plexi. And is more of a hybrid between a JCM800 and a plexi. I also, it doesn't clean up as well as the plexi, which is, again by choice because it's set to a high-gain sound that I clean up with my volume knob for a more AC/DC thing.