.clone() does just what it says. It makes an exact copy. That includes CSS styles. You cloned the
textarea to which you'd applied CSS styles:
el.style.cssText = 'height:' + el.scrollHeight + 'px';
(Note that in the specific case of textarea, it does not clone the content of the field. In the case of an input, however, it does.)
Either remove the styles from the cloned element, or keep a hidden element on the page that you do not modify and use as a source for cloning.