I may not be able to convince you, but I think I'll give it a shot anyway.
I agree with a lot of the points you make. The issue that I propose moving is a newsstand issue, and it does reprint the Ellison/Adams story from the 1990 #1. I'm surprised that "this is the determining factor here." Reprints have occurred in such a wide variety of cases (in the same title, in different titles, by the same publisher, by a different publisher, soon after original publication, decades after original publication) that I can't see forming a rule making it "the determining factor." By such logic, 1990s reprints of the EC comics would be issues of the original series. I don't think that would be correct, nor does the Library list them that way.
It seems to me the change of ownership, considered together with the timing of publication, are evidence of a distinct series. I can imagine, after the acquisition of NOW Comics by NOW Entertainment Corporation, a meeting in which new publishing strategy was determined. This is fiction, not researched fact, but I think it gets to the essence of a conversation that probably actually happened.
NEW OWNER: "We have a license to publish The Twilight Zone. Tony, you published one issue before you ran out of money. Pretty good issue, too. Harlan Ellison. Neal Adams. Big names. But the page rates you paid them! I can't authorize those rates for new work."
CAPUTO: "No problem, boss. There's lots of writers that will work way cheaper. Bruce Jones. Michael Straczynski. Me. Plenty of artists, too. Eddy Newell. Todd Fox. Enrique Villagran. Norm Dwyer."
NEW OWNER: "Good. Put 'em to work. Now about the first issue—who have we got that will really grab some attention?"
CAPUTO: "Well, uh, no one, really. Our idea last year was to invest a lot in the first issue, promote the hell out of it, and ride on that attention for the next 11 issues. Unfortunately, that was about the time we ran out of cash and, well, you know the rest, boss."
NEW OWNER: "You know, Tony, you had a good idea. Might have worked, too, if you could have kept going. What do you say, let's try it again? Can you publish the Ellison/Adams story again? And use that as a launching pad for a new series?"
CAPUTO: "Absolutely, boss. Ellison and Adams will expect reprint fees, but those will be easily within your new page rate requirements. I can have the issue out the door by the end of the week. There's just one thing though."
NEW OWNER: "Eh? What's that?"
CAPUTO: "Collectors, boss. Two issues, published less than a year apart, with the same title AND the same number. AND the same content! Collectors won't be able to tell them apart. They'll think it's the same issue we published last year, and won't buy the new one. We can do what you suggest. We just can't publish it as a Twilight Zone #1. We've got to give them some clue that it's a different issue."
NEW OWNER: "For God's sake, Caputo, why are you busting my chops with this? Publish it as Debut issue, or Premiere, or something like that. Then we could have #1 the next month. Hell, it'll be like getting two #1s in a row. God knows we could use the revenue. Now get to work!"
CAPUTO: "You got it, boss."