Thinking about something..

Perhaps, then, Joe is how Olivia remembered Jonas; in that case, Joe is simply a fragment of Olivia's memories. The KMS version of the mansion (parts of which were integrated in via 2008's event) uses the Masked Gentleman as a man who can conjure lost memories to life. That could be what's going on now.

Using this excuse you could also claim that the "evil" Jonas isn't the real Jonas from version 1 but Olivia's twisted memories of him. Angsty teens always make their parent's the villain after all and having a good/evil version fulfills that love/hate relationship dynamic.

Or we can just stick with C) Nexon doesn't care; this was written by monkeys and caters to the nx-consuming give-me-something-to-show-off Henesys-whores who wouldn't know a plot if they were sodomized with it.