I mean, is like you said about yoga, there will be poses that will be uncomfortable, at least until you achieve a level of mastery.
Being that said, if they are warning you that the procedure may be uncomfortable, then it is all good. Are you going to stop every scan mid procedure? Hopefully not, but if the patient ask, by all means.
In short, you know as well as me about the importance of listening to our bodies, and I believe the point you were trying to convey is that sometimes to achieve a particular result, it is necessary to go through uncomfortable situations.
(At some point I used to think about good pain and bad pain when riding bicycles, good pain was the soreness you felt for a few days after a long ride or a long training week, bad pain was the prelude to an injury. Sometimes it was hard to know what was what, sometimes I learned the hard way, getting injured).