"Tow & Repair All" button is available at Repair Docks - so losing a formation of 6 fighters will bring all of them back at full health,
formation is preserved, so all you need to do is issue command to their leader. All of them are combat-ready.
( Does not work for Alliance-owned though, those need one-by-one approach )

The only thing that needs to be managed manually - is cargo, torpedos, and probably carrier fighters (did not check that).

At permadestruction settings - rework of shops & upgrades is coming to make Repair Docks & Shipyards a central point for ship modifications.

EDIT:

Torpedo replenishment - holding Shift button allows buying 10x per click, UI will change to Buy(10). That's the only QoL I've found for torpedos.

Thanks for the answer LM13. The tow and repair all, is the only option after that to manually tell them to repair? (the 30% max health debuff). Thanks again, loving the mod!