I too asked this question a lot while learning how to tune these things. Here is the deal as I understand. The timing marks are ONLY a starting point to get the bow close. When cam timing/synch is set correctly, the dots WILL NOT match. The reason they won't match up is this. Our nocking point is not set at the true center of the string. It's above it. One cam will need to be advanced ahead of the other slightly in order to counter act this. If you have a draw board, use it. If not, I suggest building one. This will really show you exactly what is going on with these bows when you draw them.

Get the module draw stops on both cams to hit the cables at the exact same time at full draw. Then, look at the dots. Chances are, the bottom cam will be showing close to a half dot more than the top. ( I think I have this right)

One thing I had to contact several people on, including Bowtech was optimum cam position. This was the starting point the cams should be in at brace. For my 07 Alley, it was 4 dots. I set the bow to have 4 dots on each cam showing, then started to synch. Bow is in perfect time now and I have 80% letoff at full draw.