Soooooo the way I read it you can only have a single shields to maximum across all fleets.... And once it's dead..... To bad it's gone.

Seems weird.

If you consider that "Fleet Command" as a heavy suite of Electronics, Modifications and parts in order to enable the Effect (Additional shield generators for Shields to Maximum, Regraded Fighter Engines/Fuel Systems with C&C to assist, and the same for the Ships for Entrapment!) , then you can see how losing it would be just as bad as losing a Prototype G-8 Grav Generator.

In the all out final battle, do the fleet commands benefit all friendly fleets???

Yep!

It would be way too unbalanced if fleet commands weren't unique

Commanders only effect their own ships/squadrons even while other ships are considered to be "friendly" so I'd assume Pelta Commands are the same.

Commanders only effect their own ships/squadrons even while other ships are considered to be "friendly" so I'd assume Pelta Commands are the same.

I would assume that since they specifically say commanders that it only applies to commanders. All other upgrades affect the entire fleet.