Update on appeal
So, per above, I wrote to CBSA with a copy of their website saying the requirement had been lifted. About a month later with a little bit of time to kill at YHZ, I dropped into the NEXUS office and chatted with CBSA about it, they said the couldn't really do anything on their end (which I am willing to accept at face value) but did take the time to look into my application.
A few days later (today) I received a letter from CBSA saying that my appeal was successful, and being a Canadian citizen I was exempt from the requirement to live in Canada or the US for three years prior to application, and I was accepted into the program (conditional acceptance presumably as I haven't spoken with CBP yet) ^
They also said that it would take time to reactivate my file in Ottawa (the letter came from Montreal). We will see how long that takes. The letter was dated 19 November and it arrived 18 December. Either way, I am happy the appeal worked. I also emailed my MP about the Presentation of Persons act requiring updating to match the update NEXUS requirements.