The movement speed, range and attack rate upgrades from the portal apply to the Big Gun Ship.
With portal upgrades, the dps is the same (20% less damage per hit, but 25% more hits), but the damage/energy is more in line with other units. It is still the most efficient damage/energy weapon available: 145 damage/energy vs the 109 from ERN'ed Berthas (Airships do an absurd 1450 damage/energy).
Big Gun Ships are build in a
Manufactory, not as a building on a ground.
The cost + range + recharge of firing the sniper and missile launcher were brought in line with regular snipers and missile launchers. Which also means that ERN'ed snipers + missile launchers are better at their job than the Big Gun Ship is.
With all weapons enabled, the Big Gun Ship will burn through ammo like there's no tomorrow, especially once the portal upgrade is active. So consider turning off the sniper and missile launcher, so all ammo can be dedicated to what the ship is best at: shooting at creep with a very big gun.
The Big Gun Ship has collision detection, so no 2 (or a 100) ships can be in the same exact position. This nerf is somewhat offset by the range increase from the portal.
The energy grid connection of the Big Gun Ship is on an antenna below the ship, so that the ship has an easier time maintaining it's grid connection.