The gap was large enough we did not hit Haru even once so it did not end up particularly mattering that ninjutsu hits harder/potentially multiple targets at a time, only that he'd exhausted his chakra in 3-4 rounds and couldn't continue, instead of being able to go for 10+ rounds.
Also, melee builds tend to need less XP for the same capstone level because they dont need to invest into a dozen ninjutsu and a double-cost CP stat (plus maybe TH, we wouldn't know if Haru had it). Further, counterattacking in melee with Taij/MW instead of Athletics dodging is a thing, too. Ninjutsu are very varied obviously, so its not a clear-cut comparison, but I do think that in general the comparison holds, and the non-general cases go both ways, such as Shadow Clone + Taijutsu being a very good combination, if you can afford the steep CP cost.