Sorry - I realized my example might've been unclear since it was done in the middle of a save with mods. I ran a much simpler test on a new save with only vanilla + Console Commands. Video:
Here's what the video is showing:
Fleet loaded with single pristine Radiant with Alpha Core. Automated Ships show 240 points (60*4), as expected.
Loadout screen shows max CR is 50% with +50% from Automated Ships skill, as expected.
Pristine Radiant replaced with 5 d-mod Radiant with Alpha Core in fleet. Automated Ships show 168 points (42*4), as expected with Derelict Operations.
Loadout screen still shows max CR is 50% with +50% from Automated Ships skill, which is incorrect. Because Automated Ship points is much lower (168 vs 240), the max CR from Automated Ships should be much higher, closer to 100%.
If it helps with testing/repro, I can send the save used in the video (vanilla + Console Commands only). Additionally, it looks like other DP softcap skills might also not be correctly factoring in DP reduction from Derelict Operations as well. For example:
Here's Phase Coil Tuning with a 5 d-mod Doom and a 5 d-mod Afflictor in the fleet. The skill identifies 32 DP of phase ships in the fleet, which matches the reduced DP from Derelict Operations. However, the skill bonuses are less than maximum as if the fleet were still over the 40 DP softcap for the skill.
Please let me know if there's anything I can clarify. Hope this helps!