I thought the reveal near the end of Alternative Factor stated that the matter and antimatter universes where joined by an artificial "corridor" of space that the two ships created, that anything passing through it was converted along the way using the crystals but not actually touching.
The episode didn't establish any of that. If anything, Lazarus-B (the sane, antimatter one) described the corridor as if it were a natural phenomenon:
I call it an alternative warp. It's sort of a negative magnetic corridor where the two parallel universes meet. It's sort of a safety valve. It keeps eternity from blowing up. ... When our people found a way to slip through the warp and prove another universe, an identical one, existed, it was too much for [Lazarus-A].
http://www.chakoteya.net/StarTrek/20.htm
And Kirk and Spock's earlier conversation treated the rift as simply being a point of contact between the two universes, a natural consequence of them touching at that point.
There was nothing about anyone being converted either. The conceit of the episode was that annihilation only happened when
identical particles of matter and antimatter met, taking "particles" to mean "entire people." So that if matter Lazarus-A met antimatter Lazarus-B, it would result in annihilation, but if matter Kirk entered the antimatter universe or Lazarus-B entered the matter universe, there'd be no kaboom unless they met their identical counterparts. Which is one of the ways the episode gets physics completely, achingly wrong.
So that when the integrity of the corridor was low, it momentarily did something to the charge balance of the two universes making them neutral for a split second without physically contacting one another.
That's not what they said in the episode, and it wouldn't make any more sense of things if they had said it. (All macroscopic material bodies are pretty much electrically neutral, with positive and negative charges cancelling out; otherwise they couldn't exist as solid matter because their particles' charges would repel each other. So either a matter or antimatter universe is already neutral
as a whole.)
Here's how they "explained" it in the episode:
KIRK: All right. What would happen if another universe, say a minus universe, came into contact with a positive universe such as ours?
SPOCK: Unquestionably a warp. A distortion of physical laws on an immense scale.
So the "winking-out phenomenon" has nothing to do with anything being rendered neutral. (
"What makes a man turn neutral?") It's supposedly the laws of physics being distorted/interrupted by the temporary contact between universes through the rift at the point of contact -- with the corridor being some kind of cosmic safety valve of unexplained origin.
That the collapse of it would have then lead to them bleeding into one another causing the proper annihilation?
No, the episode itself doesn't attribute the total annihilation to the collapse of the corridor, at least not uniquely. Here's the actual, idiotic dialogue:
KIRK: Do you know what you're saying? Matter and antimatter have a tendency to cancel each other out. violently.
SPOCK: Precisely. Under certain conditions, when two identical particles of matter and antimatter meet
KIRK: Like Lazarus. Identical. Like both Lazarus', only one is matter and the other antimatter. If they meet.
SPOCK: Annihilation, Jim. Total, complete, absolute annihilation.
KIRK: Of everything that exists, everywhere.
So the premise was that if the two Lazaruses, or any matter person and their antimatter counterpart, met
anywhere outside the corridor, it would somehow destroy both entire universes (according to Lazarus-B's words later). Now, like you, I've tried in the past to rationalize that by assuming that they really meant that the local explosion would tear open the rift and destroy both universes in that way, but the episode itself never establishes that.
I was wondering if maybe you got these impressions from James Blish's adaptation of the episode, but it's pretty much identical to the original (it wasn't adapted until the 10th volume, by which point Blish was no longer reinterpreting or modifying the stories). I suppose maybe you're just taking the total conceptual mess that was the episode, filtering it through a modicum of common sense, and coming up with a rationalization that's not quite so incoherent. I've actually done much the same in the past, before I just decided that I should ignore the episode altogether (since the rest of canon certainly did).