BB,
That is a real concern and one I have encountered many times. I see a rail base as a moldable componant to the rifle. By that I mean, they are easy to machine to a specific customers needs.
When I get a rifle finished, and get ready to mount the scope as the customer wants, Many times as you mentioned the scope needs to be positioned farther or it would hit a long rail base. Another problem is that when you mount a big scope low on a rail, often times when the scope is set up for proper eye relief, the power adjustment ring will hit the last couple rail fins on the back of the rail base.
Easy cure for both, vice up the rail base, take off the first couple slots on the front of the rail for objective cone clearance and do the same on the rear. Just milling them down flush with the bottom of the rail slots offers all the clearance needed. Debur, throw in the blast cabinet and matte up and it looks like it came direct from the factory custom made for that rifle application. It its a blued rifle or coated rifle, the rail just gets teflon coated after milling.
Again, I machine the rails for each application, just want the extra meat there to allow more versitility for different applications is all.
You bring up very valid points however and points I have considered and have solutions for.
Kirby Allen(50)