I've actually found the Valis 2 manual scans I did a couple of years ago - and the story told there was indeed altered. They don't explicitly say that Megas killed Rogles, but they picture Rogles as a kind king. Actually he was the bad guy in Valis and killed by Yuko. They also picture Reiko as a "friendly ghost" and don't say anything about the events from the first Valis, and how Yuko had to kill her best friend. I guess Valis I never came out in the US so they tried to accommodate the story or something. I've updated my review page (
here) and also copied the story from the TG16's manual.
Thanks Necro for the link