You have to have a separate page sequence for any sections of the publication that you want to number differently. Leigh White's DITA for Print is a good resource.
If you set the clean.temp variable to "no", you can see the page sequences in the FO output in temp/
topic.fo
Then the real fun begins, as you search the PDF plugin for the template rules that set up the pages.
I don't recall how we turned off the cover, but we adapted the Notices page as our title page and turned off the numbering for that. In this specific case, we looked in the
topic.fo for the page-sequence with the attribute 'master-reference="notices-sequence". It lives in commons.xsl: <fo:page-sequence master-reference="notices-sequence" force-page-count="end-on-odd" initial-page-number="1">
One child of that page-sequence is "<fo:static-content flow-name="first-notices-footer">" which controls the footer.
Searching the plugin for "first-notices-footer" we found <fo:static-content flow-name="first-notices-footer">, which is where the info is inserted and formatted.