When I ream for pins in mold halves, I run a second reamer about 1/3-1/2 the depth for a slip-fit. Pins are lined up perfect and some light taps puts them the rest of the way in.
Whatever the manufacturer of the pins coats them with is a little sticky. I clean them before hand with CRC 3-36 before installing in aluminum.
If you are like me and have had a few brutal Z crashes because you ran the wrong program or thought you were on jog but instead rapid the spindle 1" into the top of the vise jaw that was 1/2" away, then you won't be as concerned about the bearings pushing in 1/4" pins. I had the Z axis encoder wheel loosen from the shaft. That was an especially hard hit since it was a runaway. I am an equal-opportunity Z axis crasher. Will do it with the spindle on or off.
I would use the VMC if I had that many pins to do. I would probably use a collet chuck with the internal stop screw. Just enough drag on the collet to hold the pin. Feed them by hand (if a one time only deal) or make a magazine (sort of like a semi-auto pistol magazine) that mounts on the table to feed the pins.
I mean if you had many THOUSANDS to place you could build a nice auto feeder that would vibe and convey buckets of dowels to line up perfectly in a picking point, a magnetic picker tool or such (slightly oversize bore with a small magnet in the bottom?), and stuff them in all day and night. You could even add a heavy die spring into your custom tool for crash safety. or an air hammer? you could do all sorts of cool shit... but not for 100.