You are correct. I believe the female protagonist is canonic in this case, although both choices are interesting as the plot and areas available differ based on this choice.And to add: in SMT If... you can pick between a female or a male protagonist, and the female protagonist becomes an NPC in the Persona 2 duology. I think it has the "If..." because it has multiple routes, so it becomes a "What if..." scenario?
SMT Imagine takes place in the SMT1 and 2 timeline. Now I don't recall if there was ever a reason why "Imagine"
My personal headcanon for Imagine is that it is a possible future after SMT2 that didn't necessarily lead into SMT3 and a whole new world conception.