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You based your amp settings on your EMGs, so the settings should be more optimal for those pickups than any others (including other EMG models). All you have discovered is that you get the most out of your pickups by tweaking the amp to suit them.Also pickups matter a lot. I get crushing tones and clarity with EMGs thru Mesa Mark V amp but Dimarzio sound like crap thru that amp with same EQ and amp settings.
Actually what I meant is for certain applications, a particular pickup fits a certain amp better. I noticed that my Fender Strat with Seymour Duncan YJM pickups gets killer tones for thrash metal and bluesy stuff when played thru my Mezzabarba MZero amp and sounds not as great thru my Bogner Uberschall. But if I play my Majesty 7 string with the dream catcher Dimarzio pickups thru my uberschall it sounds amazing. Could be a lot of things but in my studio, I’m finding my happy combos that fit my guitars and amps best.You based your amp settings on your EMGs, so the settings should be more optimal for those pickups than any others (including other EMG models). All you have discovered is that you get the most out of your pickups by tweaking the amp to suit them.
The EMGs sounding noticeably better with those settings doesn't prove whether they are better or worse than the DiMarzios, as tweaking the settings to be more optimal for a specific model of DiMarzios (which vary greatly!) would be detrimental to your tone with the EMGs.
Conversely, if the EMGs didn't sound noticeably better than the DiMarzios, despite the amp having been set up for the EMGs (not the DiMarzios), this would suggest that the EMGs are probably massively inferior (but more tweaking would be needed for a conclusive answer).
It's very possible that you prefer all EMGs to all DiMarzios, but your post implies that you haven't actually given other pickups a proper chance (not that you need to, if you're satisfied with your tone with EMGs).
If you had compared your Mesa Mark V to another amp by plugging your EMG-loaded guitar into another amp, without adjusting the settings on that amp, you would have had similar results...because you hadn't tweaked the other amp to suit the pickups. Like with your pickup comparison, it would not provide any grounds to state that one amp is better than the other - but if the other amp sounded better despite the lack of tweaking, this would suggest the Mesa Mark V is probably massively inferior (but more tweaking would be needed for a conclusive answer).