1) Nope... you can only re-arm, repair and refuel the Walruses on the island, the mantas have to head back to the carrier.
2) These improvements become available as the game progresses
3) Fair strategy... but you still have to get your walrus in to rebuild the command center, and once you begin doing that it takes a good while for the command center to become active... you're probably quicker just going through the hacking
4) The AI in this is becoming notorious! use your Mantas for strike missions, manually controlled, and once you get better armor and weapons (as well as more mantas) use them in groups to attack bases, defences, etc remotely
5)You could tell all to dock using the "wheel" and just retain control of your manta to stop it docking... Or you could just get more practice not aiming your manta at a mountain when you leave it...