Even if you have the option "Include Attachment" selected under the "Foxit PDF" outlook addin, it also won't convert the email attachment into a separate PDF file. It would keep the attachments of the selected email messages or folders as the created PDF’s attachments, with the file types of the attachments unchanged.
To convert email attachment into a separate PDF file, we suggest you open attachment in email manually and then choose to convert it into PDF file by printing it with "Foxit PDF Editor Printer".