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.
Hull Restoration plus Automated Ships is underwhelming in the first place, much as it pains me to say this. That combo gives the sadistic choice between good flagship or good fleet with only five skill points left. (I chose good flagship, and my fleet is underwhelming.) Player cannot build AI ships, so the only options when your AI ships take d-mods is to wait a long time for d-mods to disappear or pay for Restore (or respec and get Derelict Ops and not care about taking more d-mods). Automated ships cost as much as an elite ship of its class to Restore. However, the one ship that is really nice for Hull Restoration is Ziggurat. Z costs almost two million to Restore.
Automated ships are not very good (i.e., no better than human ships) without AI cores, so player cannot use too many ships bigger than frigates if they have AI cores.
Hull Restoration plus Neural Link is even worse. Neural Link has too many problems (OP tax, less flexible than Automated Ships). Ziggurat is stronger than something like two linked Onslaughts or similar.
Story points are not free when I want to set them aside for s-mods for every ship I have or especially if I want to go wild with colony improvements with doubling costs per improvement (especially for no AI in colony runs). Plus, some good systems do not have enough stable points and need five story points per point to create. Story points are not fast to earn unless the player can easily crush endgame fleets with high to max +xp% multiplier.