it doesn't make sense to pay attention to such nuances as where PI's eyes
look when the door opens, or such. The show seems to contain a lot of
incosistencies, far greater than if her eyes looked up or down. They
just put a random actor for that scene. Don't expect that level of
attention to detail, not from this show. It is also pretty obvious that
the identity of Red John was not decided upon the start of the series. The maximum I hope for is that the writers knew what was going to happen in the running season, so in S01e01 they may knew what would happen till the end of that season (regarding the RJ case I mean), in s02e01 what was going to happen in second season etc. In order to make the season interesting and to keep up going regarding the RJ case, they threw in clues throughout the seasons without a master plan, and now that the time for the reveal has come, they just don't add up. Don't get me wrong here: I still enjoyed the series, just saying that when you make an inter-season arc, you must have a masterplan in the beginning that encompasses the whole proceedings so that everything heads to an unexpected, well thought out dramatic finale.
Anyway, I hope the writers manage to explain the unexplainable in these last few episodes, and who knows, we may even get a surprise.