The question would be, how did those links in the OneBox get there? Is there harm in being the #1 search result, but not the first "result" on the page, because there's a OneBox above you with links from a different source?
As for your other question about being the #1 result but being ranked below paying advertisers, I'm not sure. Nobody deserves the #1 spot, it's not a natural right granted by your creator. In fact "the #1 search result" varies from query to query and from one user to the next based on their own Google account, if they have one.
