As interesting as this sounds, I think it is a wild thought and probably little else. I dont think the entirety of the Phoenix effect is based upon the happenstance that Bruno stumbled across an individual, error filled comic book panel. While the story also reveals Xaviers manipulations, I dont believe The Last Stand to be based off of them. Xaviers machinations via The Last Stand have long since been revealed to us before the creation and release of Deadly Genesis. Likewise, with the House of M arc. Shock deaths are nothing new, Jeans mental breakdown is the writers' take on the Dark Phoenix Saga, and the depowered mutants are the result of Whedons Astonishing X-Men.
Noting that John Bruno developed a number of character effects and their relation to the characters is not the result of being blinded by hatred. It is directly stated in an article. This is not to say that the Phoenix effect did not receive sketches or was not mentioned in a script draft. It simply indicates that Bruno clearly had a part in the development of the rendition of Phoenix that is featured in The Last Stand, which may explain the absence of the Phoenix effect, etc. Kinberg and Penn may have included the Phoenix effect in a script draft, but they maintain little to no say beyond that. Writers have no authority beyond the script they are ordered to write (particularly these two in this circumstance) unless otherwise permitted. Even then, as noted by the writers themselves, they were given strict parameters by Fox in which to maintain the story. The same may be true of Fox during any part of the pre-production, production, or post-production processes. The studio clearly requested that Bruno develop a number of character effects as well as maintain the practicality by which such powers would be displayed and how they relate to the characters. This is not to say that Bruno is solely responsible for the Phoenix effect, or a lack thereof, but it may serve as an indicator as to why certain choices were made.