i don't use auto's very much as they don't lend themselves to cloning, but i've been told (and have seen in other gardens as well) that the great thing about them not being photoperiodic is that you can run them 20:4 (or more) and get a better yield...
since they're gonna kick into flowering when they are genetically programmed to, you don't have to fuss around with the lighting...
if you have a well regulated system for pulling clones, you (depending on strain) will be much more productive both over the short term and long term just running clones from a designated mother in your cabinet...
the downside it is takes time for the clones to root and veg, but once that happens, and you switch to endless harvest, you'll be all set...
neither 12:12 from seed *or* auto's are known for their huge production qualities, but i've noticed that as little as auto's tend to produce (outside of the "ideal" indoor setup or real outdoors) they will almost certainly yield more than 12:12 from seed, as they don't get any time to veg and build adequate roots...
good luck, and be sure to post pix of what you do do, though!