I also use PyCharm but I don't fold comprehensions; ideally I don't have to since comprehensions are meant to be simple and concise. Folding a comprehension takes away all the information, including the input to the operation.
Regarding names, the example function you presented, `clean`, isn't very expressive. For example `strip_and_filter_empty_lines` would be clear about the involved operations. Naming the result instead would be something like `stripped_and_empty_lines_removed`. Not very nice, especially when you're reusing that name elsewhere you carry around that verbosity. It's easier and cleaner to name actions than the result of those actions. And again, with a function call it's clear where the result originates from (the function argument) but a folded comprehension hides that information.
One of the points of using a function is to not define it in the local scope, but in some other namespace, so it can be reused and tested. Even if you find the need to define a local non-one-liner, prefixing it with an underscore most likely prevents name clashes and even if not PyCharm will readily report the problem.