I don't think it would be helpful to augment reactions to irrelevant questions. To begin with, they are not scored. Moreover, irrelevant questions tend to be innocuous, and polygraphers don't expect to see strong reactions to them. In fact, one counter-countermeasure is to intentionally refer to the irrelevant questions as "control" questions during the pre-test phase, and then to see if the examinee reacts strongly to them.

Your anecdote about the supposed detection of countermeasures through a comparison of breathing during irrelevant and relevant questions is new to me.