I know faculty mean well when they let gut decisions dictate research choices, likely drawing from years of experience and expertise. But it puts students in a really bad position when they are the ones who have to justify those choices to reviewers and other scientists.
The power dynamics are such that a student may not feel comfortable pushing for a sufficient justification before implementing said choice in the work, or might feel like they have to use that choice even if they disagree with it.
It's a bad feeling when a reviewer or audience member asks something like "why did you do 'x' and not 'y'?", and internally you're screaming "because the person who signs my paperwork insisted we do 'x', even though 'y' is clearly better!" It also seems like bad science.
Gut choices aren't inherently bad. They're likely informed by expertise and experience, and may very well be good, in which case it should be easy to provide compelling justification for them. If you respect your students, you should be willing to have that dialogue!
And I hope we can all agree that "because I said so" isn't a good reason to do anything in science. Not that anyone ever says it so plainly, but, y'know.
(As a point of clarification, this thread is not about any faculty member in particular; it's drawing from experiences myself and others had during grad school with multiple different faculty members, with enough anecdata points to constitute a trend.)