This may be my misunderstanding but if one alters the style.css file and places it in the override directory, it should not be written to by Publii.
To reproduce the issue using the Simple theme, write the override style.css file in unminified form.
Place the file in the override directory.
“Preview Your Changes”
Check the style.css file. It has been re-written in minified form and at the same time Publii has re-written all changes to return them back to the values in the original style.css file.
Should the style.css file in the theme directory be removed to stop this from happening?