If you're going to UV the ship, you can turn the tile mapped version into the UV mapped version just by putting the tiling on the new whole map. Then bake lightmaps away.
Oh no!
That would require a lot of way too big textures.
Remeber the huge asteroid in BtRL? While it looked like it was tile mapped, it wasn't.
It used a lot of 2048² textures. Still, on close-ups, it looked as sharp as a wall in Half-Life 1, when you got close to it.
You can't bake a lightmap on tile mapped ships unless you use a lot of gigantic textures. It's a waste of memory.
The textures need the sharpness (which they get from being tile mapped), while the lightmaps do not need a lot of texture res. One 1024²-2048² should be enough for all bigger ships.
That means 4-5 small tile maps and one 2048² map, opposed to the system without lightmap, which needs ten 2048² maps, to get a decent texture res.
To bake a light map, everything needs to be mapped unique(!) The light is different on each part of the ship.
On a symetric ship, you can bake it for one side though and mirror it on the other half.