Bottom the bit in the collet, then pull it back out just a fraction of an inch...(1/16th is fine)
If you leave it bottomed out, the heat and vibration from long, hard routes can be transmitted to the bottom bearing causing premature failure.
regarding glue and sawdust filler...it really is more trouble than it's worth - The best filler for screwups is "Bondo" style lightweight autobody filler..works awesome on plywood, MDF, Particle board, whatever..:-)
cures hard enough to sand in 5 minutes, fills anything..you can place masking tape over a hole, and fill it full of bondo from the other side...wait 5 minutes, remove the tape, sand... bingo, no more hole..:-)