The thing is, I believe the cigar tip was tested before he was in custody, before they had his buccal swab. It was tested as his known sample so yes it needed to be something that one would expect to have only his DNA on. There isn't anything in the article that gives a timeframe for when it was tested. My belief is that it was collected and processed in the original batch of evidence. After he was arrested in TX, the obtained a buccal swab from him and then verified the results. But the results listed in this warrant were from the first batch of results.
The fact that stats were given to the comparison make me absolutely sure they were comparing a known from JM to an unknown from the shirt. There would be no stats given in the situation you describe.
I agree the cigar tip was "taken" from his wallet and tested before LE took the buccal swab. I DO, however, wonder where LE located JLM's wallet so they could "take" the cigar tip? If during the car warrant, the wallet would have had to be in the car. If in either of the apartment warrants, the wallet could not have been on JLM's person as I don't believe those warrants allowed a search of his person. It makes the most sense that the cigar tip was "taken" from his wallet after his arrest in Texas, but that's somewhat controversial.