The problem with using drill blanks is that they are nominally sized, and the problem with that is they aren't going to fit in dowel holes, unless the hole is reamed oversize. What you need for measuring to hole centers is a set of minus pin gauges. They are ground a couple of tenths under size so, for example, a .375" pin gauge will fit in a .375" hole, where that is not the case with a drill blank. The import sets are pretty cheap. A .062"-.250" will run you around $50 and a .250" to .500" set will run just under $100. If you don't need a whole set, they can be purchased separately but then you don't get the cool (and useful) case.
Tom