I just got my P-07 slide back from Mark @ L&M... I opted to have him place the rear sight behind the RMR in the "normal" position. Some say this is visually "busier" but I don't see it that way - hehe - it is the same iron sight picture I have shot for years, after all, and I do not feel it detracts at all from picking up the glowing orb of goodness.
I also find it easier to use the rear sight as a guide when presenting the pistol to make sure everything is lined up right. (Using the front sight only comes into play towards the end of my presentation to avoid orienting the gun high and "dropping" the front sight into place which causes the dot to come into view later in the drawstroke than is desired and in some cases can leave the dot out of sight depending on your angle of view...)
This config is best, also, in the event that I shoot the gun without the RMR... not that I ever plan to, mind you!
Anyway, I personally feel that the notion of placing the rear sight in front of the RMR came about as an attempt by some smiths to be different rather than better. $0.02