I personally tend towards building the functional parts in roughly the shape I want, then build the hull around it after confirming everything works.

I first make a feature list to map out what it’s supposed to do and what components it will need / want.

Then I try and think of a rough shape, usually the intended role gives me an idea or I just google random space ship artwork for inspiration.

Third is roughly arranging the internals for the desired shape, then some armor work around them to make a basic frame.

Next, shuffling internals and the frame shape around until everything fits well enough

Once the internals are set up, some testing of everything works as intended

And lastly, detailing and greebling to make it look good and not just a brick.

Is there a sandbox/creative mode where you could try out the different designs you're considering and prototype, calibrate, then save and use in a regular game? If so that may that may help in deciding which design you might prefer, as well as styling decisions.

Update: I decided to try mapping out the Hull and fitting blocks in afterword... It's gotten me past the choice paralysis however the hull I went with couldn't fit thrusters to make it able to handle the amount of ore it could hold. So, I've moved that version off my prototyping platform and will be starting over with the built version as a reference model as I like the overall shape. Going to use the other method of building out the functional blocks then wrapping the hull design around that.

Will post the Workshop link once it's done as I'm really liking taking a liking to this ship.