I agree.. good question. I'm aware that some of the older OE castings had mis-aligned ports (sand casting mis-alignment is common)... horizontally... the ports would jog up/down.. and IF an intake gasket is installed which has raised embossings around the ports, and IF the raised embossing would then happen to fall inside the intake rinner ports.. guess what happens... poor intake port sealing, likley vacuum leakage at any of those ports not being sealed. Typical "performance" race intake gaskets, such as from Fel-Pro and some other companies, using fiber-only type of gaskets, don't have the problem I've described. Best solution is to install gaskets having no metal-formed embossing around the ports.
It would be great if the newer casting would have been improved so to assure the horizontal aligments would be correct.