I used Derelict Operations (DO) in my latest playthrough of Starsector 0.95.1a. For those who don't know, DO reduces the deployment cost of a ship per D-Mod up to 5 D-Mods per ship. This means Moras can cost 11 DP and Legion 22 DP. This encourages the player to farm D-Mods on a small number of higher DP cost ships. You could deploy 16+ Moras or 7+ Legions, for example. Naturally since this is an end-tree skill, getting that many D-Mods on a ship wouldn't be excessively painful, but that isn't necessarily the case.
I found that story points are commonly required to recover ships after combat, especially if you only lost a single ship, but this could have just been bad dice rolls. This isn't a problem when not using DO, but it is a problem when you are. You may lose a large number of ships fighting a large enemy fleet, and recovering them can be story-point expensive if not impossible. The overall feeling I got from this was that the post-battle ship-recovery system (PBSRSystem) was designed to work directly against using DO or making often minimal use of it.
The target number of D-Mods would be 5 D-Mods. Ideally, the player would be able to add D-Mods from their colony when building the ship, since this would make losing ships and not having Story Points to retrieve them less painful.
I would really likely to see the PBSRSystem retooled to only require Story Points for recovering enemy ships.
As it stands, if I want to make an end-game derelict fleet, I just use the Command Console mod to give myself whatever story points I need to recover ships.
Now, all that said, if someone isn't using DO, this doesn't apply to them at all. This leads me to believe that maximizing use of DO was unintended when it was designed. I'm hoping systems will be tweaked to make it less annoying to use in the long term. As it stands, players are actively dissuaded from using DO via the annoyances suffered when attempting to maximize it, so they will either not use it or circumvent the PBSRSystem's requirements via mods like I did by just giving myself 100's of story points.
Then again, I've played the game long enough to be annoyed by mechanics. The new player experience will likely not be hindered until they've put in enough time to consider experimenting with niche gameplay styles.
Potential resolutions:
Player ships never need story points to be recovered during PDSRSystem.
Ships built at the player's colony via Custom Production can add be set to add 5 D-Mods.