I think that Janus could have been intended to be the original "wielder" of the Masamune. It makes sense given that Schala had Doreen, that their respective brothers would be meant for each other, too. When he was approaching Schala et al in the original timeline flashback, he could have had the red knife (essentially taking Crono's place), or Melchior decided last minute not to put that responsibility on him.
This also makes the moral ambiguity of the Masamune in RD and CC make a little more sense, imo.