That's my realization when I read Interstellar Wars.
Because if it was calculated on actual distance, jump factor one starships, if correctly positioned, can skip over an intervening hex.
Right, and that's "Jump 2", not "Jump 1".
It's just a nuance of the alternate reality of jump space.
One could argue that the star map JUST SO HAPPENS to look like a hex grid because of jump mechanics. Maybe jump space projects star systems down on to a flat plane and round them up in to single "hex" like bees in a hive. It's not a map of the stars, it's a JUMP map of the stars.
The stars really ARE in a 3D space, but the nature of jump only worries about 2 dimensions.
If, in the end, you want to put stars in places other than the center of the hexes, that's fine, but that's just going to limit Jump 1 even more, as there will no doubt be more > 1 parsec gaps in space than their are now.
No matter how you measure it, Jump 1 can't go more than 1 parsec, so there's "no way" for it to "skip" a hex.