The difference between a 3D printing pen and a 3D printer is a good illustration of the difference between craft and design ... between making and manufacture.
Using a 3D printing pen is like icing a cake ... its a craft ... design and the craft or making are one. The artefact that is made is unique every time - no two items are exactly alike ... this is the value of craft.
Using a 3D printer is like manufacturing ... indeed 3D printing is often referred to as "additive manufacturing" or fabrication. Products can be made identical time and time again - the "making" of them is programmed and automated and multiple 3D printers can produce the same identical product.
Design for a 3D printer using a 3D modelling program is technical ... this is a good thing as it brings those s=who are more technical rather than art and craft oriented into maker culture - digital designs are also great for sharing and re-mixing.