Of course, the optical part of the answer is that it does not matter. As long you can see the rear sight, you can aim accurately.
Of course, the mechanical part of the answer is that in order to avoid too much triangulation, you do not want the iron sights overly high above the bore axis. But you would need to have them bizarrely high to have an accuracy issue as distance increases.
But all of this is vastly irrelevant to the true purpose of express sights.
The true purpose of this big shallow rear V and this big fat front bead is not accuracy, it is speed, and herein lies your answer. Your express sights should be instantly visible without any visual encumbrance, for instant acquisition and snap shot as you get the rifle to your shoulder. Express sights were designed for very close range, very fast shooting at charging animals. You cannot afford to take the time to search for them among a clutter of metal on top your rifle.
If time were not the issue, much more refined micro-metric mechanical sights would be on every DG rifle. But it is not the case... Actually, many folks find that acquiring the big shallow V of the rear sight might even take too much time, and they prefer the rear ghost ring for even faster shooting: all you need to focus on is the front sight... And of course, shotguns do not even have rear sights (yes, I know, they shoot a pattern, not a bullet, but the point stands: you generally do not have the time to use a rear sight on a flushing quail...).
If your scope bases slow down the use of your express sights, they defeat the very purpose of express sights. How high does your rear sight need to be above the scope bases? Only you can determine that for yourself, but I personally do not want scope bases that hide even the lower portion of the rear sight. I find that it is OK for the scope bases to hide the rear sight base, but not the rear sight blade itself.
Just my $0.02. I hope that it makes sense to you
