The Thargoids might just be as confused as we are.
If they had the ability to create the anomaly from one of their structures at will, then they would've done that earlier in the month-long conflict in this system.
I'd hazard a guess that it's a peculiarity of interfacing Thargoid, Guardian, and monkeying around with both combining them with Human technology that caused the Structure to react in the way it does to this moment.
And it's a complete game-changer for the Thargoids.
I wasn't playing during the early days of the Thargoid story arc, but from what I can casually glean it seems the Thargoids have lost battle after battle and have lost territory after territory after the Humans found Guardian paleotech and adapted it.
The Pleiades nebula, the Witch Head nebula, and the Coalsack nebula were all lost because Humans are too good in creating very effective Guardian-Human hybrid weaponry.
Until this event happened. Now the Thargoids have gotten an I-Win button against our Gauss cannons; courtesy of Salvation.
He would not appreciate the irony of it all, I'm sure.
It's only a matter of time before the Thargoids'll be able to figure out what caused their own biotech to do this.
And then be able to replicate it.
Which'll allow the Thargoids to lift up one of their Structures, and plonk it down on a nice lowG moon in a Human system and then deny AXI units access to Guardian technology in that Human system they're in. Then, in that system, Thargoids will have reclaimed their original overwhelming power once again...
Salvation's meddling and desire to end the war in one fell swoop caused the war to be turned against Humanity...
What if the "Thargoid EMP" was "just" a side effect of the misfire and not an intentional counter-attack by the Thargoid? There are a number of possible explainations for what happened in HIP 22460:
The EMP that took the human fleet offline was triggered by the Thargoid:
-> Salvation's weapon worked as intended, but the Thargoid managed to counter it.
-> The Thargoid EMP was an accidental side effect of the Thargoid's attempt to re-activate their fleet
-> The Thargoid EMP was an intentional effect of the Thargoid counter-attack
-> Can the Thargoid reproduce this EMP effect in systems with Thargoid structures or did it require Salvation's Proteus Wave?
Alternatively the EMP was the result of the weapon's misfire and the Thargoid actually had nothing to do with it in the first place.
-> Salvation's weapon did not work as intended and misfired catastrophicly.
For humanity, a "simple misfire" would probably be the best case scenario. It was just a critical malfunction and the Thargoid had nothing to do with it.
If the Thargoid EMP was an intentional counter-attack by the Thargoid and if the Thargoid are able to reproduce this effect however, humanity could be in some trouble