On the one inch plumbing with a decent amount of flow, no. But on lower flow systems where you have the valve heavily restricting, yes.
When these systems were first developed, all three lines were at the same height, and the only difference was one pipe turned down, and the other turned up. So you may only have 1" of water over the drain. They had problems getting enough pressure to get the water over the 90 and pushing all the air out. That is why you sometimes see people drilling holes in the top of the siphon line to try to let the air escape. This is a band-aid for a poorly designed system. If done right these things really are bullet proof. If you look at it from the stand point of the pipe being in two sections, the unrestricted flow, and then after the valve where it is restricted, the water can rush much faster as start up past that first U until it hits the valve and slows down. The further away from the top of the drain the valve was, the longer the water could quickly rush down the line, pushing out all the air out. If the valve is right at the top, the restriction is at the top, and below it is just air and slow flowing water. It was a big deal in the beginning when the Bean Animal was first developed because of how it was implemented. However, today it is somewhat less important because of how these boxes are designed with several inches of water above the siphon line. All things considered though, if I had a choice, I would run it as close to the bottom as possible. Especially if running lower levels of flow through the pipe, or if I had longer runs (either horizontally or vertically).
Long story short, putting the valve at the end will always purge the air and start the siphon faster than putting it right after the bulkhead. In some extreme cases of the flow being to slow for the diameter pipe you are running, it can stop it from working right period.
I did this video today. I have another coming out more specific to our system, but I will probably only post that in my sponsor section.