I'm a little skeptical as to how the Junkers got access to Valhalla 1 (understatement of the year award candidate there). A more easily acceptable answer would be some sort of operation involving the Lane Hackers, who used to work for Ageira... Junkers being trained to interdict the parts without triggering their self-destruct mechanism.
Which, by the way, even the Lane Hackers can't do successfully as of Vanilla, and they've been trying for a few hundred years. I suppose that with the resources of an entire house behind them it wouldn't be impossible to arrange the theft of parts traveling through dangerous places like Hokkaido (not a lot of Junkers there, though) and the billions of credits in research to open them up safely and utilize them effectively. Reverse-engineering as it were. But... they can't have developed them independently. That does not work. Even reverse engineering them would likely take centuries. Read the Liberty backstory linked to here if you don't believe me or didn't catch the Valhalla 1 reference.
As for the Junkers being "just that good"... the Junkers may be good, but if they are that good then they should just commandeer all of every house's naval warships and fighters. At the same time. Without taking so much injury as a stubbed toe or damaging their new toys even remotely. That's about the level of difficulty we're talking about here. No. (By the way, those weren't arbitrary stipulations on the 'how'- you need literally perfect timing and perfect precision to open Ageira's storage containers for even the simplest parts. Perfect meaning "a few molecules off is asking for it". Read vanilla infocards, they help.)