Sub-prime mortgages have been creeping back into the mainstream for months now, but a sympathetic article that appeared in The New York Times over the weekend presented them as a misunderstood tool that helps non-standard applicants get a mortgage. Rafferty Capital Markets VP of equity research Richard X. Bove sees this as confirmation that winding down Fannie Mae / Federal National Mortgage Assctn Fnni Me (OTCBB:FNMA) and Freddie Mac / Federal Home Loan Mortgage Corp (OTCBB:FMCC) and the creation of Qualified Mortgage rules will only move the risk somewhere else. Fannie Mae, Freddie Mac: Sub-prime MBS rebound “only a matter…