I’m new to the Defold engine and want to make a 3d game, should I gather experience first with making 2d games in the engine or should I try and make a 3d game first?
Really depends on your ambition, willingness to learn and current abilities 
My first game ever was made (ok, in ASCII, but second!) was made in 3D in a very old, non-existing anymore engine 
I would really recommend starting with some tutorial if it’s your first time, just to grasp the basics. Good point to start is this section:
In particular:
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