For the H-1 engines of Saturn I/IB, it appears that at some point in development, the origin was ...almost... at the bottom of the engines, according to this drawing I found linked from AlternateWars:
That drawing shows "approximation" for the station 0/station 1 reference for the bottom of the engine bell, while another Rocketdyne document has the bottom of the engines at -1.785 inches.
So it appears that the Saturn V coordinate system inherited the definition of its origin as 100 inches below the gimbal reference plane from the smaller rocket.
A page on HeroicRelics seems to be saying that the turbine exhaust aspirator on the outboards extends "past the exit plane" of the engine, possibly explaining the outboards being an inch longer.
Another page on HeroicRelics claims that the 100-inch reference from gimbal to exit plane derives from the Jupiter's S-3D engine, an ancestor of the H-1... but dimensioned drawings on yet another page say the figure for that engine is 98 and a fraction inches.