Having covered business news for nearly 30 years, I found myself questioning a couple of things, but by no means am I certain about any of this.
1) Usually when a company takes over another company, one thing they move quickly to do is make sure they get rid of any unneeded duplication. They might even need to do that to help pay for the transaction. Even if they have bought the other company because they need more capacity, I think they usually try to focus individual plants on particular niches or product lines. So, with the situation you're describing, I would think that the two plants would be given non-overlapping specialties. The new owner would put all the bread-baking operations in one plant, say, and maybe focus the other one on making cakes and pies, or something like that.
2) Besides the cost of the "separate trip" as Iron Horseman points out, I wonder -- how easy is it to unload a specific, measured amount from a covered hopper? This is entirely beyond my level of knowledge, of course. But my first guess is that it's not that easy. Somehow I'd think that the company would seek to rationalize its supply chain procedures so that each delivery is going to be simply enough for that one plant. But perhaps there's more "LCL" traffic in the covered-hopper domain than I realize.
The idea that IH hints at, in which cars are moved internally to the company because different activities are required makes sense to me. I don't know who is responsible for cleaning a covered hopper after it has emptied its shipment (is anyone?) -- but perhaps Plant A is where all the empties are sanitized before being sent back to the supplier or something like that.
All that said, I think I "get" the idea of some operating interest created by having a car that serves two different plants on the layout. Hopefully someone will be able to suggest real life examples of that...