I've thought about this quite a bit too. It's overly complicated and headache inducing.
My solution is:
The ship "designer" does away completely with "size" categories being involved in anyway in the design of the ship's look. You simply design a ship shape putting your pieces together (not components that make it functional).
During play you assign from your library of designed ships to whatever type of ship is required: probe, colony, bb, dd, carrier, etc., Whatever you have researched.
The ship gets scaled automatically, and you modify this overall if you want. But it adds a certain number of hardpoints, etc. to which you then need to assign your actual functional components- the number and type of hardpoints is decided by your current technologies, the ship type/size, etc.
Now, obviously you could have designed a detailed Battlestar Galactica type ship and assign it as a probe and it'll look silly, but that's on you and easily avoidable. It's just appearances- it still only got (making this up) three hardpoints: engines, sensors, power source. Or whatever.
This would simplify the entire scale thing and weirdness associated with the invisible parts and invisible ship size cube starter thingy. The ship designer as is is really crap and feels like it is held together by string and gum.