I was getting about thirty plugs from a dowel using the method above. As noted, the waste piece wouldn’t quite fill a hole, but would be usable, if you were caulking and painting. It would be a bit like using backer rod (foam bead rolls) for house painting.

By altering the method, I cut way back on the waste. Pretty much to a half inch
of the entire dowel, rather than a short plug for each pocket hole plug cut.

All I did was extend how far I push the rod in and make a second cut (I made a reference mark), before trimming for length. I set the cutoff, which now has two points, one on each end, in the parallel trim slot at the back of the table (up against the adjustable stop) and the cut gives me two full length plugs, with no waste.