That still begs the question of what that other ship is. I propose a theory, which is entirely fanon so do not take it as anything but: Robotnik does have several Flying Batteries hanging around, with two known models. The Flying Battery-Base, which is the level we know that acts like a mobile base (hence the construction or at least an adequate supply of Prison Capsules), and the Flying Battery-Bomb, which is the bomber we see in Angel Island Zone. I say several because Sonic and Knuckles both destroy their own Flying Batteries, both the Base variant, hence why the level is completely intact for Knuckles' run despite the main part tearing off after Robotnik's attempt to try and kill Sonic Wing Fortress-style: it's a seperate Battery. Perhaps they are a precursor to the Egg Fleet? Again, this is just a fan theory, you can ignore it outright and say "It's a vidya game!"