I don't think these 'plot holes' are particularly hard to explain away.

Remember, the mythology we're talking about is based on what was told to very young boys who barely knew their mother by their overly stoic father. The fact that he left out details he might not have thought important is hardly surprising - and that those boys might have made assumptions that weren't entirely correct.

From a storytelling standpoint, it you go strictly by Winchester boys' canon, there isn't much of a story to tell because John and Mary are hunters at different times.