Based on the wiki and Twi's post, the Mind Flayer thing is probably not a lifespan, but a life expectancy. Mind Flayers may not die of old age, but become more likely to die after hitting a certain age.
Mhm. I'm willing to accept this, (for which I'll make an edit in the OP as a strong explanation) although they REALLY should have explored Emperor's life (and Balduran's, but whatever...) a little bit more to get rid of doubts like this. Here's the thing with the whole ceremorphosis deal - it eats away a person's body, mind and soul, so what else is left thereafter? Emperor is still behaving like Balduran - still has his memories, his mannerisms, his ideals, goals... What exactly are the mechanics of this?
