I think you are confusing two topics in your question. When calculating dose, we essentially ignore any attenuation by the atmosphere. The attenuation of air is so low for MV photon beams, that it can be ignored.
We correct for temperature and pressure because of how we measure dose. When we measure dose with an ion chamber, we aren't directly measuring dose. We are getting a reading of charge on an electrometer that we can relate to a dose reading by applying several factors.
There are different ways to calibrate the treatment machine, and to relate the measured charge to dose. The most common way in the United States is using the AAPM TG-51 formalism. This document describes in great detail what the correction factors are that relate measured charge to dose.
One of these factors is Ptp (the T and P stand for Temperature and Pressure). As described in TG-51:
the temperature–pressure correction factor...
makes the charge or measured current correspond to the standard
environmental conditions for which the calibration factor
Or, in other words: How do we relate the measurement conditions to the calibration conditions of your measurement equipment? By applying Ptp (and the other factors)
So, in summary, the measurement of temperature and pressure doesn't have anything to do with attenuation of the beam by the air in the room, but does affect how your ion chamber reading relates to dose. Applying a correction factor, Ptp, allows you to correct for this.