Is there a difference between the Outlook .MSG and .OFT file formats?

First of all, to find more information on this and related topics, move away from raw substream numbers and google for the corresponding MAPI properties. For example, 1013 is PR_HTML and 1009 is PR_RTF_COMPRESSED. MAPI has ways of synching the body from one format to the other.

See this article on MSDN for a good overview of all content-related MAPI properties (i.e. the different "streams" inside the .MSG file).

To write PR_RTF_COMPRESSED, wrap the stream inside WrapCompressedStream. On the other hand, in your particular situation you might want to avoid the MAPI-dependencies in your code, so maybe you're better off finding the PR_STORE_SUPPORT_MASK and setting the STORE_UNCOMPRESSED_RTF bit. This will allow you to use straight RTF in the PR_RTF_COMPRESSED substream. Or Outlooks fancy html-wrapped-in-rtf, if you are feeling brave.

None of this stuff is for the faint of heart, but seeing how you are already handing raw .MSG substream writing, I'm guessing it would be feasible.

When it comes to the format, there is no difference. the only difference is that OFT files have CLSID_TemplateMessage ({0006F046-0000-0000-C000-000000000046}) as the storage class (WriteClassStg), while MSG files use CLSID_MailMessage ({00020D0B-0000-0000-C000-000000000046})