#1 you can select "render selected object only" and get only the selected object in your animation sequence. Including the atmosphere unfortunately. But when I remember it right, you could as well save the mask automatically and then use this mask in your postproduction. But this is out of memory, should be verified with the manual or simply by trying.

#2 if you have Infinite you can save the render sequence as tif with embedded transparency, png with transparency etc. Then you have exactly what you need - a perfect masked single animated object.

One day your ship comes in - but you're at the airport.