I think the reason that Midnight Motorist is so confusing despite being in a game that was made with the intention of clearing stuff up could be because it was trying to clear up too many things at once. The other two big FFPS minigames have a clear focus, with Fruity Maze being about Susie getting killed and Security Puppet about Charlie, but Midnight Motorist doesn't really seem to have a clear point to it.
The Security Puppet minigame also shows pretty much exactly what we had already seen in Take Cake To The Children, so what was the point of including that? I think the point was simply to tie it to Midnight Motorist.
JR's is in the place of Fredbear's to establish that Fredbear's was already closed when Charlie was killed. The FLAF dice on the Midnight Motor car further establish that MM takes place in 87.
I think the footprints are Golden Freddy, Michael is the runaway and the line "he will be sorry when he gets back" is to establish that Michael was the subject of the nightmare experiments. The wallpaper in the Plushtrap section of Help Wanted has a pattern on it that looks like a Foxy mask which seems to further imply that Michael was the one in the experiments.
I think it's possible that Golden Freddy led Michael to the FNAF 2 location where he then discovered Charlie's corpse, but I don't really have any evidence for that it's just speculation.
I don't think the FNAF 4 gameplay is the actual nightmare experiments though, because as seen in the SL breaker room map, the core four nightmare animatronics are there but not Nightmare Fredbear. Nightmare Fredbear is also notably not present in Dittophobia whereas the main four are. And of course there’s the FNAF 1 phone call that plays during the nights.
What I think the FNAF 4 gameplay is is Michael having nightmares about the experiments he went through as a kid which are then influenced by the bite victim who appears as nightmare fredbear on night 5.
The mound is the only part that I'm kind of iffy on, I think it might be meant to be an entrance to the SL bunker, but I'm not as solid on evidence for that one as I am about the other aspects of Midnight Motorist.
