Aligning PCBA on a plastic enclosure
If the plastic enclosure is one of the typical injection molded ones available in the market they have wall thicknesses that are in the 0.1" (2.54mm) range. This thickness is not enough to firmly support dowel pins. 

A better strategy is to look for an injection molded case/box that has molded in mounting points (a.k.a mounting boss). The best ones will have pressed in brass thread inserts. These mount points can be used to accurately locate the PC board if the holes in the PC board are designed to match the box and are sized correctly.

The mounting points can also be used with additional standoffs if the board needs to be elevated.