For now, I'm raising points like that, for the most part, in sidenotes. I don't see how the remastered episodes can be safely ignored, but again, not necessarily my call.
As for T&T, I don't see how that one can be ignored under any circumstances, since we've got the DS9 crew actually in "The Trouble With Tribbles".
And "In A Mirror, Darkly" essentially picks up right where "The Tholian Web" left off, at least as far as the Defiant goes, right down to the placement of the bodies on the bridge, as well as explaining why the ISS Enterprise is essentially identical as our Enterprise (although why they haven't made any improvements in over a hundred years is another question). I've already made an update along those lines to the entry on the Defiant, but since we're still talking about a MSWord document on my laptop, nothing is final.