I don't exactly get what you're saying, and I'm also not familiar with this operation, but I would think it has to do with positive vs. negative pressure. If you're on the ID inlet side, you're taking air in a negative pressure zone, and of course you'd be in a positive zone on the downstream side of the ID fan.
So, if you connected to say the positive side of the ID fan with the "bag cleaning duct", and it wasn't being utilized or something, the ID fan would continue to force air through this "bag cleaning duct" at all times. Again, I don't realy understand the operation, but presumably this would be a bad thing. Whereas if you're on the negative side of the ID fan, and the bag cleaning operation was off-line, at least the connected duct would be under negative pressure (i.e., no chance of flue gas leakage).
This is similar to why it is best to have exhaust fans for buildings on the roof/outside, as opposed to in the space say near the source of contaminant. The overall fan pressure rating is the same either way, but there's more potential for leakage into the space with positive pressure ductwork.
Anyway, I could be way off base on this.