Senior was a muggle who was murdered by Junior, who later changed his name to Voldemort. As far as the wizards are concerned, Junior is the only Tom Riddle.
And while we're at it: Albus says "The Department of Secrets is not lightly defied," in reference to a Time-Turner. But earlier in the fic (and in canon), we have
And at the end: I'm not sure, but I think the missing period after "so she started climbing up the stairs toward her dorm room" was a mistake, rather than stylistic.
Bones is clearly talking about Tom Riddle, Jr., who seems to have brilliantly played both sides of the field as he rose to power.