If the clearance starts getting close, then it's best to use a degree wheel and dial indicator to check clearance as the clay can move around and stick a little. Typically the intake valve will be closest at around 10° ATDC. The exhaust valve will be closest around 10° BTDC.
As you mention though, the clay will show the radical clearance and has saved my butt a few times. Have had to adjust the reliefs on some custom pistons before.
I don't think I have heard anyone say that the material makes the flow different, but typically, your aftermarket heads are all aluminum, and they are the ones that will most likely yield aftermarket performance...
I have access to one of the best head porters around though....
