Yes, never scale anything but the very tips of your hierarchy.
This BasicFPCC controller works fine, see for yourself. Parent a cube one level below the top and press crouch.
If you would prefer something more full-featured here is a super-basic starter prototype FPS based on Character Controller (BasicFPCC):
https://discussions.unity.com/t/855344
That one has run, walk, jump, slide, crouch… it’s crazy-nutty!!