I'd hazard a guess that the difference has more to do with the difference in physical power sections than GEQ settings. I'd play with the amp block impedance curves though if I wanted to get a little closer. As
@My name is mud said, while the "V shape EQ" is a handy trick on those amps to get going, there really is no substitute for trusting your ears. Having said that...
If you really wanted to get granular, run some pink noise (synth block) from the Axe-Fx into the fx return of the JP2C with the GEQ engaged. Record a clip. Use a plugin with EQ matching capability (Pro-Q3, Curve EQ etc) to generate a reference curve.
Next, place a GEQ after the synth block on the Axe and set it to 5 band Mark type. Disable the GEQ on the amp. Move the sliders on the Axe-Fx 5 band GEQ until you match the reference curve. Plug those values into the GEQ in the amp block.
FWIW the 5 band GEQ measures differently on my studio preamp than my Mark IV at the same settings so I imagine an "authentic" 5 band GEQ would leave most people with the same issue of "I put the sliders where JP told me to and it's not identical".