I think Cookie is onto something, but not because of the respective animatronics appearance. Aside from the fact that they're both supposed to be representing bunnie animatronics, visually they don't have many similarities:
Toy Bonnie/RWQ has 4 fingers, Glitchtrap has 5. Glitchtrap is made of cloth, while Toy Bonnie is metallic. Neither match the teeth requirements of RWQ and so on...
Rather, Scott hinted at something in FNAF 2 that we as a community just take for granted that could be useful in this discussion, surrounding the Toy Animatronic's programming:
"As for the rest of them, we have an easier solution. You see, there may be a minor glitch in the system, something about robots seeing you as an endoskeleton without his costume on, and wanting to stuff you in a suit". Phone Guy, FNAF 2, Night 1.
At the time, we took it for what it was: an Easter egg pointing to the FNAF 1 phone call trying to explain the paranormal activities of the Animatronics. But what if instead, William programmed some malicious code into Toy Bonnie (being represented by Glitchtrap), which in turn went to infect both the new and old animatronics?
Glitchtrap in the VR game is willing to give you a birthday party (even if it's for nefarious purposes), so helping out in the Secret minigame wouldn't be out of the question. It would also explain why Toy Bonnie's model was used as a focus for all of RWQ's appearances, though why Glitchtrap decides to pick more of a Spring Bonnie appearance in the end is unclear. Maybe William's personality merged with the malicious code later on down the line during the reconstruction process for the VR port.
