I feel as though they should be all be a guaranteed recovery, really. I mentioned this in a thread suggesting the ability to cleanse them of d-mod appearance, but it's really strange that there's no further benefit in the recovery, usage or even restoration of these ships if you have the automated ships and hull restoration skills. A build that typically signals going all-in on this precise kind of ship in the fleet has no real boost to them over any other build, even in just their acquisition, which is very disappointing flavour-wise.
Because you can respec, having the ability to repair them with those two skills will make the dmods just become a time and two story point cost. Either they're permanent or they may as well be repairable normally.
Story points aren't exactly free, and if it really need be then require spending SP in addition to possessing those skills to clear the d-mods - or introduce a malus for respeccing after repairing the vessels. As it stands Hull Restoration is very underwhelming outside of being paired with Automated Ships, and that neither has
any bonus for special 'one of a kind' automated ships is just wholly disappointing. Skills should matter more in the grand scheme of things, especially in fleet composition, and offering more viable reasons to run AS/HR as your main build than keeping a Radiant would be a step in a more interesting direction.
Additionally, to return from being mildly off-topic, making all of the non-Capital vessels from that particular encounter SP-salvageable might be a fair way to let people get as many as they want without reloading the encounter repeatedly.