When the PA is on, the receiver can see the transmitter signal and can display it on the panadapter. The coupling between the transmitter and receiver varies by frequency and antenna selection. In some situations, the receiver will be slightly overloaded by the transmitter signal and so you may see the results of this in what would look like IMD in the pan adapter. Because of this, you should only use the display as a rough, relative idea for the on air signal, but should not be used to measure transmitter spectral purity. You can use two FLEX-6000s with a substantial pad to measure signal purity.
During design of SmartSDR and the FLEX-6000, suppressing the panadapter or providing the exciter signal instead of the receiver were discussed, but each of these options had clear disadvantages we felt outweighed the minor overload artifacts that may appear.