It's not clear what the original question actually is and I think in the replies two different questions are being confused. Let me reword it like this-
Q1. Why aren't big cubes the same as 3x3x3s with flat sides and covered only in squares?
A. Because during mid turn the corners would over hang completely, preventing a traditional mechanism (not magnets etc) to hold them onto the puzzle. The issue can be solved with very wide outer layers or pillowed with wide outer layers.
Q2. How is the above choice made?
A. I don't know but will guess it's a combination of easier to handle, less size and weight to package, postal costs plus less plastic.