First, from what I saw, higher level only effects performance items, like guns, shields, gens, etc. At level 40, I think you have all the shapes unlocked, outside of maybe turret weapons and fuel tanks. So, for example, when new grav drives unlock, you can just replace that 4x4 grav drive, with the best grav drive, which is 4x4. Engine lines are relatively close, but one is slightly superior. I would just go with what looks best, but you can always look up which line does what at the highest tier.
As it was a new mechanic (for a Beth game), I spent a decent amount of time in ship building, but it wasn't interesting enough to spend hours on end fucking around with my own build. So I just followed a couple ship building guides, since just building ships, from the "guides" takes around an hour. Ill let them build it, load in, run around and look at thing and fly it, then spend more time making changes.
To that effect, there is a "no ladder" build, linked a ways back, that I built and it doesn't seem like there is all that much variation, unless you want to make all habs on the same level.
Somewhat related: Flying around looking for parts is super annoying, if I was still playing I would use the mod to make all parts available for your level, accessible at the outpost shipyard.
To make a 2 story no-ladder build, you need to use the Hope Tech bridge that is 2 stories and only sold at the Hope Tech factory, then, (according to the guide) how you place the habs can determine how ladders and doors are places. The video also said that they had some issues when individually placing the ground ramp entrance with 1x1 connecting room that had the docking ring on top. So he made that section separately then used shift to move them all at once to connect to the ship.
There is also a helpful horizontal connector hallway, that is smaller than the 1x1 hab (I think), only sold at Stroud-Eklund in Neon that is probably easy to miss.
Also, just saw this when trying unsuccessfully to check the name of that Hope Tech bridge: