"Armed with a refinement of the piece of technology that caused the Universal Cataclysm Disaster... They able to destroy the extra-universal threat and finally 'reclaim' their own universe"

This.

This is a two fold advantage. One it gives a reason for the Collective to have survived, having been able to stave off the threat after tens of thousands of years of endless war. Two: It gives a good reason for why we can actually return and not be curb stomped by the evil extra-universal Empires. The barrier between the Primary Universe and the tertiary universe were reinforced, locking the aliens out. While it likely wouldn't stop them forever, why bother trying to break reinforced walls when you can just go break standard ones and invade a separate universe? Especially when you know the technology exists that was able to beat you the first time.

Now, how is this tech not overpowered? One: It is designed only to work on extra-universal signatures. Potentially you could invert it, but it couldn't tell the differences between species, only those which are native to the primary universe and those which aren't. Two: Its one of the most resource intensive pieces of tech Three: It took over 10,000 years to get it to the point it would only attack the reapers without essentially causing the apocalypse. While it would obviously be shorter now they have fixed the universal apocalypse problem, it would still require a ridiculous amount of time to reprogram it for another race. The Collective only managed to survive long enough the first time round because it had two major advantages the other races didn't.
The first is Psionics. The Collective were able to survive so long because they had psionics. The ability is highly versatile and played an important role in both battle and the construction of the weapon (Details to be released shortly, I am working on a short story styled thing to just post here about that)
T