Was it agreed upon by both companies that although Namor could not resist it fully, that he could resist Arthur's powers partially due to his unique nature? If so the same would apply to Namora no?
You got me on that one. I'm just wondering why it didn't make Namor pass out, while the rest of the Atlantean's took a snooze? To me it was like both DC and marvel agreed or came to an agreement that Namor or those like him could somehow resist. Maybe it's within their mutant ability? All the same, if they aren't able to, I agree with your first post, but if not, i could see Namor's side pulling a few wins.
JLA/Avengers might be worth an exception. Marvel has mentioned it (obliquely so as to not touch DC trademarks) in guidebooks. DC went a step farther and actually had the Trinity mini-series follow up on events in JLA/Avengers (Krona and the cosmic egg).
More to the question at hand, I'll echo my sentiment from the Mera/Namora thread. If they just duke it out, Namor and Namora should win. However, Mera and Arthur have some other tools at their disposal that could carry the day if they're clever about it.
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It was also mentioned in a Photon bio too, iirc. Either way, I wouldn't consider either to be canon for either company. If it can't be canon for both, I don't see how it can be canon for one over the other, because then Superman is fighting some facsimile of Thor, not Thor himself.
Anyway, in a physical battle, yeah, they're outmatched (though Arthur is going to tank a hell of a lot anyway based on past events), but when you bring in anything else, Arthur and Mera should take it imo.