Hello,
I have built the SE-2s, so I know exactly what you are trying to decide. I went through the same sort of mental gymnastics myself. In the end, the best answer to me was to remove as much material as possible with the flare while leaving behind just enough material to feel good that the driver mounting screws have plenty of wood to bite into. This is a judgement call. I don't recall exactly what I used, but my cabinet baffle thickness wasn't as thick as yours either.
This will take some trial and error. Just start with a small cut and slowly increase the router cutter depth/radius. I could be wrong, but I doubt that anyone will be able to answer your question directly. While you may hear a difference between no flare at all, and the largest possible flare, I doubt you'd hear a difference between a "middle of the road" flare and the largest possible one. I know that doesn't answer your questions directly, but maybe it helps a bit.
By the way, I don't think a chamfer bit is recommended. I belive a roundover bit is preferred, but I'll let the cabinet building gurus chime in on that. Good luck!
Rick