I can't tell if you factored in the happiness to keep the city delight, so I run the calculations myself with using these stats:
10 BCs running a cicle of two 8h, one 4h and two 1h it gives you more supply than having 12 Junkyard doing the same cicle
BC- 758268
Junk - 696532,8
12 junks consume 5244 pop + 7341,6 happiness for pop + 6000 happiness + 240 squares + 48 roads (and produce 696532,8 supplies)
10 BCs 6660 pop + 9324 happiness for pop + 5000 happiness + 250 squares + 50 for roads (and produce 758268 supply per day)
If your using bungalows:
Junks need an extra 47,88 tiles for pop itself plus another (5244 * 1.4 / 122,5) 59,9 tiles to keep that 5244 population delighted
BCs need an extra 60,82 for pop plus another 76,1 tiles to keep the pop delighted
Now the extra breaking happiness is 49,0 for junkyards and 40,8 for BCs (this is for breaking happiness alone. I don't see where you got the higher numbers unless you added the other happiness or tiles taken with it)
So Junkyards need (240+48+47,88+59,9+49,0)= 444,78 tiles for 696532,8 supplies = 1566,0 supply per tile per day
BCs need 477,72 tiles for 758268 = 1587,3 supply per tile per day
(Weird, I never got more for the BCs before, but I don't ask for motivation of my own supplies, so maybe that was it). anyways, junkyards do 1,34% worse than a BC. That is a very, very small increase (and large cost) from PME to CE which was why Huscarl probably considered it bad (though I would personally put it under good)
EDIT:
Duh, I was using condominiums for my population. That's why I'm getting different numbers. I get Junkyards are 2.5% better than BCs though