The "bad" file's CSS is a complete mess. It has hundreds of @font-face (mostly unused) and styles with unsupported properties, not to mention unnecesary <span>s, etc. There are also font names written with " instead of a quote mark, which I suspect is wrong. However, the main thing that could affect font sizes, is the fact that font sizes are hard-coded in the CSS.
I've cropped the styles and created the attached file, it has two "chapters". The first one is just as it was, so I guess it will scale incorrectly. For the second, I've modified the styles, removing all font references and explicit font sizes, my bet is it will scale correctly. Of course, coming from Word the HTML-like code is utter crap (not your fault, though, but you'd be better copying the unformatted text in Sigil and formatting it there).
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