I think you want your stops in quite a way from where your guides are, 6" or more. Logs are rarely ever perfectly straight. If you have your stops directly in line you need the log to not sweep outside the backstop line, or have a trimmed limb, or a fragment of wood from digger grapple or whatever etc lying outside that line. Also need them high enough to reach the widest part of the log, which isn't necessary (otherwise again, some log lies outside that line).
Bringing them inboard doesn't reduce the size of log the mill will take, you can always lower them. If you've got a 40" log on the bed you're not going to have the stops up at 20" high, that is impractical for all sorts of reasons including needing to turn the log earlier than otherwise, if plain sawing or slabbing. Usually I have my stops sitting down at about 10" max, and the tip of them touches between say 7-8 o'clock of the log looking at its face. If you need to shift it over further, go lower on the stops.
I went dead below my guides first round and found out it was a mistake the first day I got sawing. The pockets are still there, I thought no harm in leaving them in case they are ever needed, and just added new pockets about 6" further in. I don't recall ever using them.