Ughh, yes, I guess that's essentially the same. I don't think I quite followed your proposal earlier. Well, I think it's going to be fiddly and weird however we do it, so we can just take your suggestion.
Underbar: Pilot Advancement
When determining the XP earned by the pilot, determine an effective CR for each opponent the juggernaut fights. First, subtract the juggernaut's opponent's CR from the juggernaut's CR, then the effective CR is the sum of that difference and the pilot's CR. Then use the opponent's effective CR to determine the XP earned by a character of the pilot's level.