The Opportunity Analysis RCE report type is reporting just on standard SFDC Opportunity information. It is not using Marketo Program information so FT and MT are not considered. The origin of a Marketo lead has nothing to do with whether the lead is associated with an Opportunity. This report type shows Marketo leads (which at this point are SFDC Contacts) and their associated Opportunities. In order for the Opportunity to show up, the SFDC Contact as to be associated with the Opportunity thought the Contact Role. This can be confusing and some sales organizaions aren't good at making sure this happens. If an SFDC Contact is associated with an Account but has no role on the Opportunity, the Opportunity will not be reported on in Marketo.
The Program Opportunity Analysis report type shows both Opportunities and Marketo Program influence. There still has to be the association of the SFDC Contact to the Opportunity through the Contact Role for the Opportunity to appear in Marketo reporting. For this report, again, the origin of the lead doesn't matter, you can still see MT based on the Marketo Programs the lead because a success in before the Opportunity has closed.
Hope this helps some.
Sheila