Nice changes, seems like a reasonable streamlining.
I was thinking on the salvage Gantry, it would be interesting if the ships would have dual function both in salvage and in field repairs, in the latter case perhaps giving the fleet an efficiency on supplies for repair or maybe repair times? Honestly, I am sorta surprised we don't have a military Yardship, that is to say a moving repair yard. given the distances involved you'd think the factions would have dedicated support ships .
Hmm - anything that mitigates supply/repair costs is a potential problem, since those costs are there for a reason, so it's just something to approach carefully. If it just becomes another "lug this around to reduce costs" ship, then that's not very interesting, right? And if it's just repair times, it's probably not worth it. But if it let you do something qualitative, it could be interesting.
it could be a little bit of both, a tiny amount of one may not be enough to justify something, but a tiny or small amount of both may make it worth while.
you could also either make it non stackable, with low a maximum bonus limit, or a small stackable bonus with diminishing returns, I think it's worth experimenting.
on a side note in the lost fleet series by jack Campbell, had tenders and auxiliaries that were capable of taking scrap, mining asteroids etc and turning them into supplies for the fleet.
How about letting the salvage gantry, or other specialized ships have a small nano forge on board, (or allow you to mount one when you find it), which would allow it to turn scrap metals and or raw ore into the equivalent cost of supplies, or more likely, at a little less efficient ratio, say 125% material cost into supplies. The production speed needs to be limited say enough so so salvage gantries and similar ships could noticeably help keep a small fleet supplied, but be practically unnoticeable in a large fleet.
if you're worried that may break the supply mechanics a bit, keep in mind when you start a faction you can make a factory to produce supplies right? so it looks like you’re going to be finding a solution for that problem anyways.
another thing the salvage rig, (or a specialized mining rig) could do is quick & dirty mining on asteroids and planets. since you're not there to make a permanent mining station (could you? #faction gameplay?) but for the quick and dirty you'd just be scraping off the exposed deposits on the surface of the asteroid or planet and heading off.
Heck, that gives me a thought, why cant we salvage ruins on planets? it could also give you a use for marines if there is any de-civilized populations, dangerous animals, pirates, or other scavengers around.
also, one or more military fleet tenders would be nice, you could make it a little less efficient than the civilian rig, but generally speedier, more stealthy and capable of defending itself.
Finally, ships with mining/salvage drones, do they reduce casualties from salvaging accidents? if not, they should, I'd use them over a person in a risky operation any time, could give players a reason to keep a Shepard in their fleet for the bonus.