The fact that the line moves "faster" after the FP merge point is simple logic and math, although there is subjectiveness to what "faster" means. It's certainly faster than the standby line was. Not faster than the Fastpass line. And some lines are observably different like at RNRC and Soarin' as you stop and wait for quite a while a couple times.
But lets take the simple example of, say, Buzz Lightyear's Space Ranger Spin. It is a "continuous loading" ride, with a continuous queue. And let's say it loads two guests per second.
If there were no fastpass line, the entire line would move at the same speed - two guests per second.
With a fastpass line, after the merge, it still moves at two guests per second.
The merge point itself can let through only two guests per second as well. But now it has to do so proportionally from the Fastpass and Standby queues.
If the Fastpass issue rate was, say, 50% of capacity, then they are going to need to let half the people in from the Fastpass line, and half from the standby line. Thus, the standby line now slows to 1 guest per second.
Issue more Fastpasses, and it slows even more.
But here's the trick - the standby line is obviously slower, in the sense of velocity. But it's also shorter, in terms of number of people in it - since a lot of people who would have been in it are instead using the Fastpass line.
If everything was proportional - a guest using a Fastpass would otherwise have been in the standby line, and only does it once, went shopping, etc. then the standby line should take just as long as it did before.
Where it starts to fail is when guests use FP multiple times in the same attraction, get in other lines while Fastpass is holding their position, etc. when they otherwise would have gone on the attraction only once. THIS is what makes the standby line overall longer.
And I think FP+ might actually change this for the better, due to the limits on usage (not saying the limits themselves are good, but in terms of the flow).
They _may_have been issuing more FP/FP+ in total than before as they introduce the new system. It's hard to tell for certain, but subjectively it seems true. I don't know if they will reduce back to "normal" once the transition is complete.