Strict adherence to formatting rules can impair readability, yes.
Before back-tick strings in JS, it was useful to employ both single/double quotes for strings -- you'd use one most of the time, and then if you needed to embed a bunch of that quotation mark in a string literal, you'd switch to the other one.
'my string'
'my other string'
"insert values ('foo', 'bar', 'baaz')"
A formatter with naive "single quotes only" rule would obliterate the last one to: 'insert values (\'foo\', \'bar\', \'baz\')'
unless you remember, before you hit save, to add a directive like: // linter pwease preserve my qwotes
I still use linters and formatters every day, and on balance I think they're good to have, but it's ridiculous to pretend they don't have downsides, or that there isn't room for the occasional dash of human intervention in the automation; hence, the linters which have // linter pwease directives.