Reviewing your sources.... "MSM in Africa" does not contain the string "trans" anywhere in the document.  I don't know what you expect in that document being used as a reference, except to increase your refcount.  UNAIDS states that "TG is typically considered alongside".  It is fairly equivocal about the whole matter.  The Powerpoint Document gives the most convincing argument with the statement: "With regard to HIV surveillance and prevention, the CDC’s current practice is not to separate MTF TG and TS people from the MSM category, with no attention paid to the risks of FTM TG people." (A noted lack of source on this in the document is noted here... it amounts to hearsay.)  The MSTGW article speaks against applying labels such as "MSM" and categorizing people.  This would include the MSM label.  That the article specifically refers to these individuals as "MSTGW" and not "MSM" is a good indicator that TG individuals would be non-MSM.  Lastly the HIV-releated Tuberculosis document specifically states that the individuals are male and that: "Some network members dressed as women and participated in dance and fashion competitions known as "balls." These social networks include "houses" (i.e., a guild providing a social framework for young MSM and transgender persons) that exist in many large U.S. cities (house leader, personal communication, 2000). All four also were commercial sex workers."  This is clear information pointing to that these individuals were drag queens.
My conclusion... I have to admit, I've been viewing TG too narrowly, and excluding individuals that are TG, yet also MSM.  However, that doesn't mean that TS individuals are MSM... it's hard to argue that a drag queen isn't MSM, while it is hard to argue that a post-operative MTF living a life in stealth is an MSM.  Please feel free to alter the document to reflect this information.