Proper way to draw the bottom plate and counter top through Rhino.Inside?

Proper is always going to be contextual, depending on the project requirements and what you are inputting.

DirectShapes are great, but do have limitations.

Check out this script for doing a sweep in a family document [New GH nodes] Family.Extrusion by Profile, Extrusion.Attributes, Family.Parameter - #10 by lukabergs

I’ll see if i can get a handle on Caio’s issue in that thread in the meantime.