I also use pins for precise placement of fingerboards or peghead veneers that are already with binding and must align perfectly or for repairs when you don't want the edge to overhang the neck. I dry clamp new board in place and drill tiny hole through two slots for pins. On repairs I drill the holes before i remove the board.
I wouldn't drill holes in guitar bridges/tops or any sensitive part of valuable instruments (I would even consider not drilling into neck - where there's no real danger of damage) but use other ways to prevent misalignment. Also for longer working time I can rise temperature and humidity in my workplace for the needed time so glue is liquid for longer.
Fish glue cen be produced from various fish species and that aks for inconsistency some of the valuable species of sturgeons (traditional source of bladders) are almost extinct and not all species produce glue with same properties, some may be more hygroscopis some more elastic etc... That's why good ole HHG is the most reliable.