I described a scenario like that in one of my earlier walls of text, but let's take a look at how you see it:
That particular scenario would, of course, require the CT quest to be completed, as the tower has technically been "awake" for the five years since its return to the surface.
Reread what you posted, and yes, they could have two different variants, but I can't imagine one that wouldn't cause issues when the questline is done in parallel with the CT storyline. Unless they put it somewhere else entirely but call it Eureka just for the hell of it, in which case, "what did Nero's scanner pick up?" is left as an unresolved question.
Putting aside discussions on how they decide to pull this off in continuity, I think if the "opportunity" Nero is pursuing is related to his declaration that he will be the one to surpass Allag, if you consider the current seal on the tower to be a "test" to see if Allag has been surpassed, it could be him opening the tower to start the Eureka storyline. There's a weird sort of one-sided rivalry he feels towards G'raha at the end of the WoD scenes that I'd like to see expanded on in some form.
