First of all, I would like this to be the last comment from both of us, because we have found exactly where we disagree and there is no need to continue. So I think we should leave the rest to the staff.
No, no, no. They didn't go to the first timeline. They went back before that timelines branched out, before Ben Prime reached the Omnitrix.
Here's what I think you're missing. After Paradox reboots the Prime timeline with NW Ben, after he delivers the Omnitrix to Ben, Paradox tells him that this is why they also rebooted the Vilgax timelines. And this point is exactly where the timelines of those two began. Ben getting the Omnitrix and Vilgax losing the Omnitrix. I think what I misrepresented above is that this is the point where the timelines for both Vilgax and Ben start to "branch". And where these two are going is not another multiverse, as I mentioned in the previous message, but the past of the tree that was destroyed in the present, before it started to branch out. CTB just erases these branches and the Prime timeline from the "present" time of what you call cross-time, but there is still this tree in the past of this cross-time. And you don't need an extra axis to go back to that past. Because this is not a situation that requires a different axis. They still go to a regular past.
There are no different versions of this tree. The tree just has a past, present and future. And these in cross-time still contain the same axis of past and future as trees. This is exactly the " doesn't count" option in QAW's diagram.