Keep in mind that, the purpose of using rails is to remove all that force and stress from around the glass optic. That's a good thing. In terms of scope height, this system developed when Mauser 98's had swing safeties and the scope needed to be high enough to allow the safety to swing through it's arc. Also, if you look at older Germanic rifles, there is often a see-through under the scope, so you can use the open sights with the scope in place. This is from an era when scopes were not as reliable, and if they were fogged up, you had a 'Plan-B'. Also, on combination rifle/shotguns, you didn't have to use the scope to shoot the shotgun barrel - especially if the fox or other critter was too close to be in sharp focus in the scope, or perhaps so close that the scope was actually aiming above it. Also, the scope mount often had the windage adjustment built into it, there being none on the scope.
Some of these designs have been superseded by more modern developments, such as side or tang safeties that allow a lower mounting position. Modern rail scopes have a choice of different styles of rails for lower mounting, for this reason. So you can have the best of both worlds.