This is so odd. I updated to K4Mac 1.21.0 to experiment, and I'm still getting AZW3 straight out of the box without having to do anything special (i.e., no Terminal sudo chmod).
I've confirmed twice that I really have 1.21.0 installed. I've deleted all my downloaded books. I've made sure the books I'm re-downloading say "Enhanced Typesetting: Enabled". And yet, I am still getting AZW3 (Alf confirms this).
Also, I'm on OS X El Capitan, if that sheds any light on things.
Not complaining, just curious why this is happening