The tools can't exclude a bunch of irrelevant changes if they're submitted with the code to be reviewed. Instead of the submitter doing a little extra work they're forcing the reviewer to.
The tools can't explain why changes were made when a bunch of commits have a single comment that doesn't explain anything, like "feature completed". Instead of the submitter doing a little extra work they're forcing the reviewer to.
If everyone learned to use the tools well there wouldn't be these problems, obviously, but it's clearly not as black and white as "Commits absolutely do NOT need to be some coherent chunks".
So don't commit irrelevant changes to your feature branch, this falls upon the "blind commits" -category of problem.
The best way to explain why certain changes were made is not in the commit messages as you should not review separate commits but the end result of the work in the feature branch.
What I do if some change is unclear is usually one of the following:
Oh and if you don't know which of the changes you made are relevant to your feature branch anymore you don't commit often enough.