Jason was really dead. He was brought back to life (by Superboy Prime punching time retroactively, but that doesn't matter). So yes, there were magical forces at work. But "make no mistake, it is him", in the words of the narrative of Batman Annual #25.
I think Neron must have thought about the issue and decided Bruce would be even less likely to agree to his parent's return than to Jason's. Bruce is as aware as the reader that his parents' death is Batman's origin, and such a offer would ring more alarm bells that just bringing Jason back.
Also, Jason's death was unnatural in a way Thomas and Martha's murder isn't; parents aren't supposed to bury their children, after all. Neron's playing on the guilt chord as well, and while Bruce sometimes feel guilty for his parent's death (according to the writer or the version of the story), he was responsible for Jason.