1) None of the ending texts are canonical. This is well-established. It is common for the next game in the series to start from a point that is similar to one particular ending, but it is never identical.
2) We know from Litalia's autobiographical spiels that Ghaldring emerged before the end of the Shapers' razing of Drypeak. He obviously didn't die there, so that's already one exception. It's not hard to imagine that Rhakkus happened to be on a mission outside the valley when the razing began, and didn't return. He's been an unprincipled and self-centered character from his first appearance, so this is quite plausible.
I agree that it makes no sense for him to disappear entirely for two games and then have a dialogueless cameo in G5. However, it's possible -- if he stayed in Western Terrestia and just didn't happen to cross the PC's path until the end. I agree it seems unlikely, and I would still assume that Ghaldring shaped an assistant and named him in honor of one of his forebears. But we can't know for sure.