Personally, I prefer using 'Edit book' to the viewer's inspector. Calibre can significantly rewrite the HTML as part of the pipe line that converts all the different formats before handing it to the viewer renderer.
Ideally, you'd only put replace_tags_with_spans in for the sites (or stories) you need it for. But in practice, <pre> tags aren't actually used much anymore.
I'd actually
add <pre>, rather than replacing the existing settings, like so:
Code:
## the comma(,) is necessary
add_to_replace_tags_with_spans:,pre
I assume you know that you have to update the story (or download anew) before the replace_tags_with_spans change is applied?
Without knowing even the site you're trying to use, or seeing your personal.ini (there's a button to get a version with user/pass settings removed), I can't help any further. It's working as designed for me.