Janus is mentioned by the elder... unless I'm mis-reading your post.

Elder: When the disaster struck, an eerie, black portal materialized. Melchior tried to save Janus, but he was also dragged in.

Sounds to me they were both pulled into their respective gates. How the elder knows this is beyond me.

But anyway...
I think it's a given that both originally and after Crono's death Janus was still sent to pre-600 AD. If he hadn't the second time around then a gargantuan paradox would happen and the story would literally fall to pieces.

• there would be no Magus
• there would be no war
• there would be no Leene abduction (which would interfere with Crono's first viist to 600 AD)
• there would be no rivalry with Frog - Frog would still be human
• there would be no incentive to get/fix the Masamune - therefore Ayla would not have been found

...and on and on. Magus is crucial to the story, so if he doesn't get sent to the Middle Ages we have a pretty big problem. Just the fact that after he joins you his appearance remains as Magus tells us that he must have still arrived in the Middle Ages. If he hadn't he should appear as Janus, no?

As for the photograph, I've heard many sources say the man in it is Serge. Apparently the artbook has a better picture of it. Either way I think it was ridiculous to not show his face in the game.