you want to know the temps inside the cylinders. the farther away you get and the more things in between the less accurate that's going to be.

 

you want to know the temp at the ports i'd think. otherwise how do you know if you're burning outside the cylinder or not?

 

you're a wiser man than I so I'll take your word for it. The port or close to it is the placement of the sensor so that is effectively what you're measuring. And sure the reason for an EGT gauge is to know when you were getting into piston melting territory and/or the nature of the mixture's burn otherwise.