You're only getting the page_styles.css created/linked during calibre conversions because that's how your calibre conversion preferences are set. Change the settings for page margins on the convert Page Setup page if you don't like them.
Be careful of setting all page margins to zero as this might prevent the Kobo font adjustment margins slider from working - if this is important to you. Experiment before doing any mass reconversion.
You can remove or change the page_styles.css files in existing calibre library epubs by running the 'Modify Epub' plugin with the 'Modify @page and body margin styles' option checked. I think your current calibre Preferences are used to decide whether to remove or change page_styles.css.
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