same here ... mine is started to look like i have freckles on my hood with all the touch upsFor something small like that I don't bother with primer or clear on top. Just use a good touch up paint with a brush. The pens are worthless. My objective is to stop the rust, not make it look good.
My experience has been if I want it to look perfect or close to I'm far better off to spray the entire panel. Way too much work for a touch up job.