Reinforcements seem to come from any available factory. If you have factories on repeat or the queue is already full, reinforcements come from the other available factories.
I've been experimenting with building factories closer to the front lines and destroying the ones back in my base, so the units don't have as far to stream.
I would be cool if we could set a factory rally point to a specific army. Any requested reinforcements only come from that factory(s) with the rally set.