I think Peter Farrelly was looking for a way to disengage from this whole situation with Jason Mann, and saw an opportunity. After all, Farrelly was the one who was actually offended by Jason's pushy and non-humble response to winning, and certainly as we've seen, Jason's a total pain in the a** to work with- this fight with Effie was the perfect excuse to get away from a difficult production and mentoring a director he didn't like.
Or he's a total spoiled baby who packed up his toys as soon as he was challenged!
Totally agree with you that Effie's negative reaction to the first phone call completely blocked her ability to really listen to what Farrelly was saying in the second phone call- he was trying to help production by getting Jason to be onboard with film, rather than forced into it, but Effie was still mad at his earlier meddling (when he wasn't acting as a mentor for Jason, but questioning producer decisions like tax breaks and filming locations) and so took what he was doing and saying completely wrong. She was right in the first phone call, but wrong in the second.