Probably multiple ways. One way I can think of would be to play a steady tone into the amp input with some kind of device like a tone generator. Then take an output either from a flat-response mic in front of the speaker, or perhaps the headphone out, and put the output signal into a DAW with an oscilloscope plugin cued up. Then manipulate the Tone knobs until you flatten the EQ curve as straight as possible. I probably wouldn't take an output from the XLR out in this kind of test because the cab sim feature cannot be defeated and might skew the results a little bit.
I would assume they got the EQ out via the FX Send, which is directly after the EQ stage (see block diagram).
