Not really.Yes but I honestly think it's an error to think that since there's tube amp modeling in the Axe-Fx the IR's shouldn't be done using tube power amps. Just think about it.
If we are talking about subjective preferences then there's no right or wrong, just your own personal preference.
If we are talking about faithfully emulating a specific speaker cabinet and only the speaker cabinet (this does not presume any subjective preference by the listener), then no it doesn't make sense to capture an impulse response with a coloring amp (tube or not).
You can capture the impedance data as well, which you can translate into the amp block's speaker tab to more faithfully reproduce the interaction with that specific cabinet driven by a specific amp.
Wrong. See Javajunkie's response.The only way that would make sense is if the Axe-Fx power amp simulation is modeling what happens to the cab when driven with different power amps but (correct me if I'm wrong) don't we have a separate cab block and the power amp simulation is not affecting it?