To reiterate and emphasize – OP’s son DOES qualify for federal aid, because unsubsidized federal direct loans are federal aid.
Again, to reiterate and emphasize – Tufts is the exception, not the rule. A small minority of schools (including, apparently, Tufts) have a rule that institutional need-based aid will not be awarded to continuing students if the student did not apply for such aid in the initial freshman enrollment process.