When calculating takeoff performance why include airport elevation in pressure altitude?
If the altimeter says the station pressure is 29.92" sea level, but I am at 3000', then the airplane still thinks it's at sea level when it comes to performance. Is that wrong?


Although the station pressure may be reported as 29.92", that does not mean that a barometer there will show that as the current pressure.  The reported value is the actual pressure, plus an extra amount that is calculated would occur if the recording station were lowered down to sea level.  Instead of actual pressure, you are setting the QNH pressure.

So sitting at a 3000' airport with the altimeter reading 29.92 does not mean the airplane thinks it's at sea level.  Certainly the altimeter doesn't think this, because it's reading 3000'.

You could use the actual pressure outside as an altitude-independent performance gauge, but you don't normally have that value (and ATC isn't going to radio it to you).