The attachments are not embedded. It is called inline or viewed in place which is different.
When attaching image/photo attachments and smaller PDF attachments (1-2) pages, these type of attachments are shown inline or viewed in place within the body of the message by default which cannot be turned off - when sending and receiving.
You can control-click on a viewed in place attachment and select View as Icon. Regardless, all Mail.app attachments are sent as true attachments to the message.
Depending on the recipient's email client and available preference settings, such attachments may appear inline or viewed in place with the message is opened by the recipient (as with the Mail.app) or as attached files only which must be opened separately for which we have no control over.
I prefer this feature since it ensures that I have selected the correct image/photo attachment before the message is sent and I always add all attachments after I've finished composing the message below all text.
You can use a 3rd party Mail.app plugin called Mail Attachments Iconizer which can be downloaded at the following link.
http://lokisw.com/index.php?item=MailAttachmentsIconizer
Regarding the two attachments that appear, the extra attachment is the Apple resource fork for the file which is invisible to fellow Mac users. This doesn't occur with all Windows users since it depends on the Windows version and email client and version the recipient is running.
Beginning with Panther (10.3), the Mail.app includes a send Windows Friendly Attachments feature.
Check
Windows users have problems with files I send and be sure to include the filename extensions, such as .doc, in the names of all files you send to Windows recipients. This way the files can be read by a Windows application.