We all know that Bonnie was Decommissioned sometime AFTER entering Monty Golf because the Afton Virus was messing with his coding through the message titled "MISSING"- "SECURITY REPORT - 12:24AM - Bonnie is seen leaving his green room in Rockstar Row heading East towards the atrium. 2:40AM - Bonnie enters the East Arcade. 4:12AM - Bonnie enters Monty Golf."(https://freddy-fazbears-pizza.fandom.com/wiki/Dufflebags)
Now, what we can tell through Context clues is that, despite the upfront personalities of each animatronic, Their code stops them from actually hurting each other and the Pizza Plex Guests When Freddy says "Gregory, Those parts belong to my friends. I would never do anything to hurt them." and, "... They are not capable of hurting a guest. None of us are. It would go against our programming." The Voice lines, Combined with the Security Report and what we already know from the previous games in the series, Supports William being Behind the other animatronics going against their programming, Becoming Hostile towards guests. But, there is one more piece of evidence I have.

The Original Spring Bonnie, The Ultimate Guide

The ORIGINAL Spring Bonnie shell would have been completely destroyed after the fire in FNAF 3, and so would the Scraptrap shell in Pizzeria Simulator, Where Afton was before Security breach.

Scraptrap as seen in Five Nights at Freddy's: Pizzeria Simulator

Now, what we can presume is that, per Fazbear Entertainment protocol, No GUEST is to be able to see an Endo out in the open, and since Afton is practically fused with the endo at this point, he felt the need to get a new shell (Not to mention being a walking Corpse). The only problem is that an animatronic suddenly disappearing would be far more suspicious than, say, an already troublesome animatronic attacking him. Now, as previously mentioned, the Afton virus messes with the code of all the animatronics. So, instead of Monty just simply telling Bonnie to get out of his attraction, Monty, through the influence of Afton, would destroy Bonnie, thus causing Bonnie to be Decommissioned and Monty to be the new bass player of the band and Afton gets to have a new Shell. Now, You may be wondering, "Isn't Burntrap already in the Spring Bonnie shell?" to which I say NO!

Burntrap as seen is Five Nights at Freddy's: Security Breach

If you pay attention to the character designs, Springtrap Doesn't have shells for his feet, where as Burntrap has one for his left foot. Not to mention that going from the Scraptrap suit to Burntrap, you can see unexplained healing around the cranial area of Scraptraps suit, although a foot is lost in that transition (As for the sudden growing of an arm, He would've also gotten that from the Decommissioned Bonnie.) One more thing to mention: Missing copper wires going from Scraptrap to Burntrap. TL;DR: Afton had Bonnie go to Monty for Decommissioning.