The bird starts 1 pixel to the left in Bizhawk. I captured this using the Stella emulator, which has a frame advance feature in it's debug mode. The birds X position is at $61. In BizHawk on the frame the bird appears, the value is 0x4D, in Stella it is 0x4C. Other emulators agree with this position.
But you don't need frame advance to see the differences, here is a another screen shot of the countdown, the number '1' is pretty clearly one pixel to the left in Bizhawk:
It's not the ball that is positioned wrong either, it is at 0x55 at $5B in both.
I suspect there is an emulation issue in Bizhawk.
Returning to the problem at hand, in my opinion, we need a way to classify these total control and similar runs. They need to have their own rules regarding completion criteria, as well as overall criteria on what is allowed and disallowed. I find a key factor here that games which lack these exploits are finite. Baring loops, there are a (nearly incalculable) finite amount of ways to complete a game. However, in games that we can add our own code, once we do so, there are now an infinite amount of ways to proceed. These two groups are now objectively distinct, and we really do need to come up with a set of rules for each. These rules we develop should take into account how the different groups of these runs differ from each other as I entailed in my presentation of the previous problem, and allow for many runs per game, but limit the infinite. An important point to consider in developing a tier and rules for it is how a run makes use of the existing game once its payload begins. This run to my knowledge is the first run to no longer make any use of the game whatsoever once the payload begins. Meaning that the final payload can be ran on any SNES game once controller input to RAM becomes possible. Since it's not tied to a game, do we accept different runs of Notepad attached to Super Mario World, Super Metroid, Kirby Super Star, and others? Not only do we have to categorize what kind of diversity we allow for any given game, we need to limit how we apply this diversity to many different games, as I do not wish to publish the same virtually identical payload over and over. I already began work in trying to define a new tier for these kinds of runs in order to spark some discussion. However, I find this initial work to be lacking in that it does not make use of yet to be developed movie class/branch criteria, and it does not supply a series of rules on how to deal with the aforementioned sub-problems in this tier problem. If we can iron these issues out, I'd be happy to enable the site to support it, and then accept this run if it conforms to the new rules. In closing I want to add that runs like this which include payloads and play them take tool-assistance to their epitome input-wise, and we should put the effort in to properly acknowledge them.