I like granularity but I don’t know if this adds anything more than a hidden system for less knowledgeable players to lose efficiency in.
It would only be as hidden as Alex would make it to be. If it was an icon in the upper left corner of every ship slot, like all those buttons are at the bottom of it, it wouldn't be hard to spot.
Phase ships, civilian ships, etc. are all operating under global fleet bonuses. I think these are set up the way they are for a reason. Imagine having a phase fleet and only giving the phase mastery bonus to a Doom flagship. I just don’t think that’s how it was designed to be.
The phase skill is probably the only one that would bring any issues. I guess you could unselect Crew Training for officers with Combat Endurance and extra CR from industry's whatwasit? Otherwise, it would just allow players whether they would want all their ships to receive equal bonuses, or if they want to maintain an elite core and average reinforcements. And more importantly, it would show players that they aren't "punished" for having a large fleet, only that even fleetwide skills are finite in their scope.