Of course the real Big Bad isn't Ms. Marigold! Remember that she's based on Nightmare, who, while a legitimate threat (as is she, financially), is all in the Bite Victim's head, after all. What's Nightmare's description in FNAF World? "This is why you wake up." In fact, her embezzlement is ultimately what caused the victims of Jeremy Human's to wake up from their self-imposed complacent pity party.
Bonbon being the bunny most attracted to Mike actually does make sense if one remembers that, in FNAF canon, "Toy Bonnie" was the first edition of the Bonnie model; Weaver Bonnie may have her yandere on for Mike, but she would have inherited that from the female Toy Bonnie.
We're never told what happened to Mangle, but Frederick's drawing of them cowering before something looming over them implies that they ran afoul of a humanitronic. If it was Fritzine, perhaps she, ahem, removed a few...parts from them (external or internal) and the trauma affected their body image/gender identity.
More of a Fridge Sadness. Roth/Ruth was right not to let someone who seemed to be an unauthorized lunatic serve cake at Jeremy's. However, she a) made a scene in the middle of a busy children's restaurant with loud swearing included and b) stormed off to get the day manager, allowing said "lunatic" to serve the cake anyway. Although she seemed to very much need her job and want to keep it, it would have been pretty unlikely, even if Fred and April didn't shut down the franchise in the epilogue.