I don't think you can mimic the modded muff as they are about modifying the pedal's tone stack for the most part and the muff tone stack is about filtering the mids away (tonestack = parallel HPF & LPF having the tone as mix ratio). But you can always try and probably atleast get closer.
Any way I can mimic that on the Kemper, or do I just do it by putting an EQ block after the Muffin stomp?
I would start with this approach yes. Recall there was tubedriver in his chain after modded muff so could try e.g. some GS there as well.
I don't know which what muff version the Muffin is based on (different versions have some variations in the tonestack), but as a starting point one could maybe try counterbalancing the BM "Civil War" circuit where the mid dip center is around 1.3KHz so the GEQ's 1.25k knob would be my first choice. Followed maybe also Low and High cut tweaks with some volume to compensate.
If the GEQ works at all (maybe even with a Green Scream as a booster/filter) I'd next grab Studio EQ and tried to sweep the Hz value together with its Q-value to finetune the Hz band and center point.