Couple of observations about Johnny Boy:-

Hesh Rabkin comments in Season 1 that Johnny Boy, despite being younger than Junior, was a made man first.

Tony makes the point to Melfi that Tony, at barely 40, is 10 times more successful than Junior who 'still lives in some shitty house in Bellevue.' Though Johnny Boy never attained the success that Tony achieved, I always felt there was an implication that Johnny Boy's crew was:

a. involved in more profitable rackets than Junior's which Tony inherited to a certain extent and

b. Had top earners like Big Pussy and Paulie while Junior's crews always had their share of goons.

Additionally, Johnny Boy would have benefitted from the sage, if unofficial advice of Hesh Rabkin throughout his tenure. As I recall, Johnny Boy was said to be close to De Meo -- hence his ascendancy to made guy before Junior.

Moreover, as Capo de la Cosa Nostra sensibly points out it's unwise to look too hard for consistencies.