I've definitely sunk skill points and money into ship building, and my problems with inventory are a lot less now that I have 3000+ on my ship. It will be better eventually, but my ship is a bit of an ugly mess right now. Since leveling up the ship parts skill requires buying unique parts, it incentivizes doing things like buying lots of parts that don't match, or finding cheap parts that can be stuck on without affecting much.
Be sure to make your ship on an outpost. It has more options. You might need to buy some parts elsewhere though but slot is located in Outpost launchpads.
I was able to build a solid A class ship based off of someone endgame C Class build. I have no points in shipbuilding stuff, but i got a very nice ship that performs well and can be upgraded.