Yep. The HT not taken into account bit in the OP is...silly, unless that means "assume optimal HT on both sides." After all, the HT determines the quality of the blade, let alone whether it's a blade at all.
3V is considerably more expensive, in both materials cost, and in machining. So, while ESEE and Ka-bar do a great job with their 1095, and for that matter, I do really like 1095 because it's darn good for what it costs, that doesn't mean it's in the same category as 3V done well. It's just a lot more cost effective.
As for being at the mercy of the maker, I've gotten the impression that a good many makers that use 3V, also send their blades out to Peter's or Bos for heat treat, both of which are as well known for doing a good heat treat as Rowen is for 1095. I would certainly be more nervous about a 3V blade where the HT was done by the maker than I would be about a 1095 blade where the HT was done by the maker, just because the 3V is a more complicated steel, with a more complicated HT process. But I can't imagine there are that many makers who specialize in 3V who don't either have it professionally done, or else have put a LOT of time into testing it and refined their process. It would be foolish and expensive to specialize in 3V without getting the most out of the steel.
And then to turn around and say that "oh, we're leaving out makers who *specialize* in 3V," but then turn around and cite Rowen, who it can be fairly said, specializes in 1095... well, that's a bit hypocritical, is it not?
So...all things being equal, assuming ideal HT on both sides for the blades, if price is no object, 3V I think would clearly have to be a better choice. The thing is, 3V isn't cheap. An ESEE made from 3V would likely be VERY expensive, and most non-knife nuts already consider ESEE's to be expensive. Is it enough better than 1095 to merit the increase in cost? That's an entirely different question, and would depend on the user and the use.