its because the regestry isnt on the mesh, the part your seeing is an OVERLAY of the reg-mesh ie Nacelle_logo in max sacuer_logo for an example... the textures is a totally different part as well,
there is also another mesh inside it self for damage, bc dont use this,,,delete it
So here we go, lets try and right this in english
The regestry mesh as i stated above with the _logo tag is actaully another part of the ship mesh Hoving very slightly over the top of the ship. this flying part of the mesh use's another texture alltogether normally found to be (as an example) F_Yorktown_logo1.dds (readable in photoshop with the nvidia plugins) now if u remove the hoving reg mesh u wont see that gray part... u could then texture stright onto the ship.... this is somthing u will have to do due to bc not using the same method as legacy...Since i was head modler at UUM i kinda made my name for my self there so this is kinda my fortay
...if u need anything add me to skype and i'll talk u though it..