What this will do is make it so 2 theaters are "more or less" dedicated to Fastpass, but there's no reason for them to arrange the line in a way that this has to be adhered to all the time. Fastpass distribution is typically 65-70% of capacity. If the merge point allows you to send guests to one of 3 theaters, there's no real reason to reconfigure the line when it's not needed.
Conversely, the queue for Toy Story Mania very well may have to be reconfigured as a result of the 3rd track. That explains why they may have been doing the Fastpass+ only test to see when they sent out empty cars.