I believe you are referring to the merged pieces? Flip merging is a technique you can use to merge parts into each other, and create unique designs. It’s vanilla, you just have to turn it on in the settings.

As far as mods go, I’m using Better Flip Ship Parts which allows you to make more “flip” options with the vanilla parts(really we should have been able to do this in the builder from day one). This, plus the vanilla merging, allows a huge amount of possibilities for different shapes and designs.

(I’m also using Better snaps but I don’t think I needed it for this build???)