Is the gain from IIP3 curves wrong?
You need to understand what the VSG is calling its Pout, the amplifier's Pin, when there are two tones present. It might be the total (thermal) power (+3dB(single)), it might be the peak power (+6dB(single)), or it might be the power of one individual tone (0dB(single)). You should be able to find out in its operating manual. Or, you could find out by measuring it with your ADC without the amplifier in circuit.

Presumably the Pout obtained from spectral analysis of the ADC on the output is measuring the power of any individual tone, regardless of how many there are.

I am a mistrustful curmudgeon, and will routinely check what a source or analyser is doing when making/analysing a complicated signal by direct measurement, when there is the slightest possibility of uncertainty. It's also nice to 'warm up' by making a measurement for which I know what the answer should be, just to check I understand everything before trying to measure a device I know nothing about. I continue to be surprised at how often the warm up measurement throws up an unexpected problem in the gear, the cables, or my concept of what their readings mean.