I think it’s more likely that Greg Mendell’s an alias Owen Flynn’s using. Greg’s certainly playing bad Mulder with Storybrooke, I doubt he’d be using his real name as people might remember him from back then.
I bet he lost his father in Storybrooke in mysterious ways (AKA Regina crushed his heart, don’t ask me how that would happen in a magicless town, I have no idea) and he’s been trying to go back find out the truth ever since.
ETA: as far as the dynamite goes, I think the better question would be: what happened to the security procedures that comes with dealing with explosives? Any 11-year-old can grab them? Should we expect to see Henry wielding a submachine gun next? 🙄 😆