From what I have seen after the Forsaken update, regarding the time to kill for auto rifles and sub-machines, they haven't had the body shot damage correctly scaled. In Destiny 2 Year 1, the auto rifles and sub-machine guns had about a 30% critical multiplier and not a 60% critical multiplier. For example, the Ghost Primus, a 600 rpm auto rifle, in the Crucible at optimal range, did 17 damage to the head and 13 to the body (about a 30% difference). Enter the Forsaken time to kill update and it does 21 to the head but still only 13 to the body. I further believe this to be an over sight because on the Destiny 2 combat reveal stream (https://www.youtube.com/watch?v=fdylZ_1Vj-M&t=1180s) at 41:08 Cozmo used the Ether Doctor (a 600 rpm auto rifle) and said "even with the body shots, you can see a difference" when in truth there was no difference in body shot damage from Year 1 to Year 2. I believe the change to make auto rifles do 30% critical damage instead of 60% and to have their body shot damage increased was in Destiny 1 Rise of Iron, because auto rifles were harder to land consistent head shots compared to the other primaries. This was grandfathered in Destiny 2 Year 1 with the auto and sub-machine guns and it would be greatly appreciated if it went back to that especially for sub-machine guns.
Handcannons and pulse rifles outshine autos consistently in crucible because they are peek weapons, there is no such thing as peeking with an auto rifle. In order to match, auto rifles would need to be buffed as you said