I put the spoiler tags on that MOS story synopsis above, so no one will get offended.
Usually, Clark is described as the survivor from a destroyed alien civilization. Not so here.
It seems to me that it STRONGLY implies that Krypton was not destroyed in this version and it is simply an advanced civilization from which Clark was "transported" from.
Since in this version, Clark must wrestle with either saving humanity or "divide and conquer", I think this may mean that he was sent to earth as some sort of sleeper agent in order to prepare it for invasion.
This explains why Zod and Faora would have arrived in Smallville.
For all we know, Zod and Faora imprisoned Jor El and Lara on Krypton and are attempting to manipulate his son (a la Chris in Last Son)...
Hmmm....