Regardless of how you go about it, make sure to do the doweling before the taper is cut--which is sorta how I read your post but I wanted to make sure to mention it.
As long as both adjoining ends are square, straight and smooth--I shoot mine with a plane--and one can hold them together and see that there is a seemless fit, and assuming the dowel is straight into both sections, the join will be good all the way to the dowel, all the way around. So once tapered it should look nice and clean.
I typically chuck the pieces into my vise and use a brace to bore the holes. I shoot for a hair over-sized on the holes so the dowels fit OK. Not so loose they can simply fall out, but not so tight they need tapped in. I turn my own dowels to get that fit. The slight looseness allows the parts to clamp tight at the seem. I use epoxy for the glue.
Take care, Mike
Wenzloff & Sons Sawmakers