This article 3D PRINTING AND LEGOS: PERFECT TOGETHER is a great example of an engineering principle that says that you should only be precise where precision is necessary. Unnecessary precision is a waste of time, money, and resources. The article shows a prototype of a pair of goggles, where precision is needed for the areas holding the lenses. So they used a combination of the Legos (cheap, easy to work with, and abundant – but not easily modified) and 3D printed pieces (takes longer to make each one, but you can tweak them until you get it right.)
So yes, 3D printing and LEGOs may indeed be perfect together, but the real story is that any time you are designing something, you want to pay the most attention to the parts that matter most.