Pepperboxes and needle variants are functionally different guns. Pepperboxes are more useful for dealing high damage to a single target, while needles are better for peppering at long range. The charge is even more different; needles either hail gunfire at a group from a long distance or shred something at point blank range, whereas pepperboxes' vacuum effect sucks a single enemy in from moderate range and hits it with the rest of the bullets, emulating a point-blank needle charge.

They're two different guns, unlike different branches of other trees that just change damage type and status effect. My Blitz Needle comes out in FSC, where it's awesome, but my Volcanic Pepperbox gets brought into RJP and arenas to quickly take out turrets or extract critical enemies like menders from a horde.