According to what you've written, it looks like the two universes are inextricably tangled, and your assessment that they should be merged in the tagset is correct.

Mod W's assessment is that Alt/Original Timeline specifications should be kept, like in any other case where there are multiple variants of the same character in one canon. This still means that (Either Timeline) should be split into one or the other, however.

I'll leave it up for any further thoughts or comments until tomorrow, then merge the two other fandoms into it in the morning if there's no further dissent.