That's because it's using a lot of hard-coded divs with specific widths. it would be an FR for calibre to handle these, there was actually a discussion about doing this in another Calibre thread for a similar formatted book:
https://www.mobileread.com/forums/sho...d.php?t=107107
An alternate pdf converter (same div problem, but does a better job in some respects, the one you linked is a bit better in others, as the underlying html appears to be un-wrapped):
http://convertpdftohtml.net/