Thanks Horizon.
The variants of the Vengeful Spirit and Scion of Prospero just change the stats of existing weapons modules, so don't require the swapping of weapons modules. In hindsight magnetizing the Despoiler was pretty dumb given the lack of possible variants and the in universe fact that only four Despoiler type ships were ever built and all of them are named ships.
As a side note, I also have problems with Vengeful Spirit and Scion of Prospero being Despoiler based, given that the only Despoiler style ship in existence at the time of the Heresy was the unique Terminus Est.