So i think i thought of a way to use up all that extra hangar storage you end up with (end game period) due to simply scaling up ships size over time.
Hangar Fighter Storage Bay, not a block, maybe a... sub-menu? in the hangar tab of your ship.
In this space you have the ability to pre-build your fighters, which are then stored in an inventory like arrangement? From here you can move a fighter to your fighter squads (perhaps where the blueprint would normally be) thus selecting the type of fighter to be loaded, the squad will then autofill with any fighters from your Hanagar Fighter Storage Bay, until none remain of that equivalant.
i always felt the fighter squads and production were quite janky, they serve their purpose, but i feel like this would fix a lot of its janky-ness.