If you plan on spraying in a garage, and you plan on possibly getting some dust particles in the basecoat, then chances are you are going to get even more in the clear (since the clear dries much slower then basecoat). Your best bet is to tack each basecoat as you go, then go ahead clear it.
Now, if you are talking about a situation where you plan on spraying a color like white as your basecoat, then getting dark colored particles in it, then of course clearing over this would do you no good since these will really stand out. Even wetsanding the basecoat would do no good either since the dirt is in the base. Also as mentioned, if you wetsand a metallic base, there is a good chance of disrupting the way the metallics lay. This will really stand out once your clear.
Your best bet is to do as I mentioned above and that is to tack off each coat of base as you go, then go ahead and clear directly over the base without wetsanding. If you use a true basecoat, most of these dry very quickly. So any dust that lands on it, you will be able to tack off between the coats.
You will be able to wetsand any particles that land in the clear thus giving you a nice flat finish.
Scott