I tested it and it's what I theorized, the splat version of the NJP has a 0.95 damage scale instead of the 0.8 damage scale of the launching version, that's why the damage from the combo is different.
Basically every number after the NJP is multiplied by 0.95 instead of 0.8. You can divide the damage of each hit after the NJP on the less damaging version by 0.8, taking into account that some might be rounded one decimal up or down, and then multiply them by 0.95 and the damage will be the same than each of the hits on the more damaging combo.