Thanks for the question.
I am not an expert in Domino or MIME, but the Mail Merge agents do not perform any special conversion. Although the default format in Notes is Notes Rich Text, it should support HTML/MIME just as well!
I expect you are seeing different results due to your Notes/Domino configuration relating to how it converts Notes RichText into HTML MIME for external internet addresses. I believe The Notes Client settings would be used when you manually click 'Send', but (as Vladimir discovered earlier) the Domino Server settings would be used when sending through the Mail Merge agent.
Firstly, check your Lotus Notes Client configuration:
File -> Preferences -> Locations -> Edit Location -> Mail -> Format for internet addresses: = MIME Format
File -> Preferences -> Mail -> Internet -> Internet Mail Format: = HTML and Plain Text
Secondly, check your Domino Server configuration wth reference to the relevant IBM InfoCenter documentation:
Message Format: = Convert from Notes to HTML - Domino converts the text in a Notes rich-text document to HTML. If the message contains file attachments, Domino creates a multipart/mixed MIME message and includes the attachment in that part. If the message contains images, Domino includes the images in the message body by creating a multipart/related part. If you are experiencing problems when MIME messages are rendered within an IMAP client, use this setting or use "from Notes to Plain Text and HTML."
Hope that helps. If not, please provide some screenshots of the message you are trying to send and the results and I'll try to help where I can.
Update 9 May 2013
Our users were having the same problem recently sending email with Rich Text tables to internet addresses where the Domino server has default Plain text conversion. I discovered a fix for Notes 8.5.1+ users ONLY: Modify the SaveAndSend method of these agents to call doc.ConvertToMime as below:
Description: Saves and sends the document
Public Sub saveAndSend(doc As NotesDocument)
doc.SaveMessageOnSend = True
doc.PostedDate = Now()
'Convert RichText fields to HTML + Plaintext
'Syntax: notesDocument.Send( attachForm [, recipients ] )
I will investigate adding this function to the next release.