This decision would affect the order the stages are played in the last 30% of the movie, although the contents of each stage wouldn’t change bar RNG manipulation.
In-game level map:
https://mario.wiki.gallery/images/3/3f/WL2_Treasure_Map.png
Stage IDs and how they actually connect to each other:
https://user-images.githubusercontent.com/19356108/78606033-78854b00-7811-11ea-9d38-239099972cab.png
Basically, a normal exit (vertical arrows on the graph) unlocks the "next" stage in the order of the internal stage IDs. 6 normally unintended unlocking (24-25, 29-30, 34-35, 39-40, 44-45, 49-50) can be done via OoB normal exit. All level completion that doesn't involve unlocking the "following" stage is triggered by a "secret exit", and this includes all 6 ending sequences in the game.
The movie is currently at the point after Ch.4-5, where the 3 Final Chapters and Really Final Chapter are left. To finish the game in a more "conventional" manner, ending with the ending sequence from Really Final Chapter, we would use the following order:
20 -> 21 -> 22 -> 23 -> 24 -> 40 -> 41 -> 42 -> 43 -> 44 (beating this via a glitched exit unlocks 45) -> 45 -> 46 -> 47 -> 48 -> 49 (after this the "GREAT!" scene is played, which normally unlocks Really Final Chapter and jumps the cursor on the map selection there) -> 50
Or, to save a net total of around 90 frames by leaving the "GREAT!" scene out of the inputs, we could do this:
40 -> 41 -> 42 -> 43 -> 44 (beating this via a glitched exit unlocks 45) -> 45 -> 46 -> 47 -> 48 -> 49 (beating this via a glitched exit unlocks 50, Really Final Chapter, prematurely) -> 20 -> 21 -> 22 -> 23 -> 50 -> 24 (after this the "GREAT!" scene is played, and the movie would end on this screen)
The ending mechanism in this game has been explained in my previous post. Stages 24, 29, 39, 44, 49, and 50 each has an ending sequence that would be played when the stage is beaten normally (or via an OoB secret exit). In a "100%, inbounds" movie, the first 5 ending sequences would be skipped because there is more to be done while the last would be allowed to play, both because it is the last one in the intended order and because, well, there is nothing left to do anyway. If we do the sequence break to play Really Final Chapter (50) early, its ending sequence would be skipped not because anything is preventing it to be played but because of the simple fact that there is one more stage to be done. In fact, the stage we would be doing the last, 24, has its own ending sequence, and this one would not be played because it's faster to finish the level via an OoB normal exit, which doesn't trigger the ending sequence, and there is no available OoB secret exit that was found, which could have triggered the ending sequence while still skipping the boss fight.
The closest case among the published movies that I can think of is
[2027] SNES Donkey Kong Country 2: Diddy's Kong Quest "102%" by Dooty, NxCy & Comicalflop in 1:21:31.88, which uses some method to complete the normally post-game ending first while triggering the intended first/any% ending at the very last to keep it out of the inputs. The movie jlun is working on would do something similar if the route with sequence break is done: it would end with a screen that signifies some sort of completion that normally wouldn't be the end of the movie to cut it out of the inputs while still finishing all gameplay contents supposed to be done. So maybe the real question here is,
does the screen shown in the screenshots posted by jlun count as a completion screen of some sort that can be used as a valid movie ending point if all the intended contents of the category are otherwise done?
Additionally, this movie is intended to be a new "100%" category in parallel to the existing "100%, inbounds" movie, which does have the 6th ending sequence of the game played out at the end. IMO, it is better to use the sequence break route in this "glitched 100%" movie to show off as much brokenness as possible and make it as different from the other 100% category as it can be, especially when, as mentioned in the previous post, the main benefit of ending the movie with an ending sequence in this case is more so to show a screen where 100% counters along with the best time record for the Really Final Chapter are displayed for formality, not that a specific ending sequence in this game is functionally unique.