Beginning with ship(s) instead of planet(s)

I sincerly doubt it.
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There are 10 types of people in the world:

Those that understand binary, and those that don't.

Maybe not directly, but there ought to be a workaround. You might be able to have a way for your one planet to have really really low happiness so it will riot and revert to its own empire. If you want something like Battlestar Galactica (which I would totally love to help with), you need the whole planet to go bye bye. So maybe you could start with black hole tech and make a ship (or two or however many), lift off and make a black hole, or planet destruction, whichever tech is easiest. That may not be ideal, but it would work.

Does any one know how to mod with scenarios? This may be what your looking for.

Scenarios don't exist.
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There are 10 types of people in the world:

Those that understand binary, and those that don't.

Scenarios exist... Just play all empires as human, set up what you want, convert AI empires back to AIs, save. Bam, you have a scenario.

If you have SE4, take a look at the space monsters in Devnull. They are pretty much what you are looking for, I think. They do make use of a single planet, but total lack of troops and colony ships means all they do is build (maintenance free) ships to send out. Their HW is cloaked via a level 99 sector - sight obscuration component on bases, so you can not attack it directly.