[Akula]

I think there's a fenomenom in Cataclysm called slipgates or something similar, the Cal Stooh (not sure about the spelling) uses one of those for a far jump, those could propably serve as some sort of warppoints, it's not a great explanaition, but it's not entirely away from the HW universe, without having to rely solely on the Eye of Arran
Also about constructed gates, I think a large part of the Bentusi escaped through some sort of massive gate a good way into the cataclysm storyline

Actually radiation fields might be a very good explanaition ofr storms, don't they also affect sensors?

A thing to note though, the Dreadnaught isn't a unique ship, Makaan also has one he uses to open Balcora gate, this raises some questions, are there more than one mothership? Or are/was Dreadnaughts generally used as progenitor warships.
Also one might think that the Vaygr somehow has some sort of compatible matrix, after all Makaan is so bend on getting a hold on Sajuuk I really doubdt that he'd waste the time trying to get things like it's weapons systems operational, also as mentioned before the Taiidan also know the word Sajuuk, if I remember correctly they're the only ones that uses it in HW 1, thus there are also some things that point to the Vaygr having some relations to the progenitor