What bothers me about bonuses with low caps, such as Phase Coil Tuning, and the carrier skills (and what Tactical Drills used to be with +10% and a 120 OP limit) is not the distribution of the bonus across multiple hulls, but the lack of fine control. If these skills worked based on what you have deployed, that would be one thing, but having a situation where a ship is weaker because of the mere existence of another ship that's not even part of the battle... annoys me.
Edit: Like, say I'm cruising around with the Ziggurat as my flagship! I pick up Phase Coil Tuning, Elite Field Modulation, etcetera; really focus in on being the best phase ship pilot I can be. Now, what happens when I end up in a battle with some random dinky pirate fleet that really just isn't worth deploying the Zig? Well, obviously, I swap over to a cheap lesser ship. Thematically, this should be another phase ship; perhaps a Harbinger. Practically? I cannot afford to have another phase ship in my fleet, because that will weaken the Zig when I'm using it, and dramatically weaken said other phase ship when I'm using that instead of the Zig.
So I'm going to suggest that - where possible - these skills should be changed to be based on what you have deployed to battle, rather than what's in your fleet overall. As an added bonus, doing this would make it make sense to return Tactical Drills to its initial +10% damage at 120 DP.
Exceptions:
• Bulk Transport and the fuel/supply usage bonuses from Containment Procedures / Makeshift Equipment are entirely non-combat skill effects, and would make no sense to scale with anything other than your full fleet.
• The sensor bonus from Phase Coil Tuning is also a non-combat effect... but one that can be partially or completely 'lost' due to how sensor mechanics only consider the values from the top five ships. In short, this sort of bonus already has capped scaling from just how sensor mechanics work, and should not
also scale down as your fleet grows to include more phase ships. I would suggest changing this to a flat +120 sensor strength bonus for the single highest sensor-strength phase ship in your fleet, with no DP-scaling involved.
• Field Repairs and the crew-loss reduction from Containment Procedures should simply work at their max effect. These are not highly-valued skills, so a small buff like this isn't a balance problem.
• Crew Training is the annoying one here - due to how max CR is implemented, it's not practical to have this depend on deployed forces rather than the entire fleet. I would greatly prefer if this skill just gave a flat +15% max CR to combat ships (or, perhaps, non-automated combat ships? That sort of limitation feels thematic, but would also require some re-balancing of the Automated Ships skill given how it uses CR limitations as an internal balancing factor). However, the skill's already over-budget for being a mere tier 1 skill, and just flat buffing it doesn't feel like the right call to me either. So... not sure what the right answer is here.