Taking it from the top:
You awake in Crono's house, Lavos has entered the Earth in 65,000,000BC and the Zeal palace incident DID occur and throw Janus and the Gurus to their respected times.
Warp to 600AD
The Janus from the normal timeline has ended up here and has become a very powerful wizard/mage. He is known as Magus.
Warp to 12,000BC
After the incident at Magus's lair, Crono and co. and Magus are thrown to random time lines. Magus disquises himself and proclaims himself a prophet. His knowledge of the past, being Janus from the original time line, earned him the respect of the queen. Crono and co. intervened and history repeated itself. Another Janus was thrown into a gate.
So somewhere near 580ish AD, Janus has come into contact with Ozzie in another time line aside from the normal time line.
What I am trying to get at is, some where, some time, another Janus/Magus exists. Does this also mean that another Schala is linked with another Mammon Machine?