The best way is to overdrill, but put in a G-10 insert instead of a dowel. You can then tap into the G-10 and it will never be a problem and you do not need to glass over it on the outside.
We buy G10 at McMaster Carr, but a quick web search turned this up
G-10 supply
You can get the stuff in sheets, rods, whatever, and it is very tough, holds a thread, and is easy to work with. Great material for quick fabrication. I also use this for engine mounting holes-overdrill and then put in a G10 tube and you end up with a compression tube that will not allow the transom to be compressed by some mechaninc with a big wrench. Just leave it a c.h. long after you glue it in.
I would worry about putting wood dowels in-how is that any different than the plywood you already have?