The facts are clear that crankcase gases can be a significant component in the intake charge. See:
http://www.camaro5.com/forums/showthread.php?t=328400. Other direct injected engine manufacturers have their hands full as well. Toyota had some very public engine varnishing issues on their traditional port injected v6's.
With traditional port injected engines gasoline additives are usually effective in cleaning valves. I use Shell or Chevron for filling up. However there are still issues with coking of piston rings, and reduction of engine octane resulting from crankcase gases.
Do crankcase gases affect the LS3? In my experience - yes, in terms of affecting octane. Even with the 1LE clean side separator I still experienced audible pinging. This kept the engine from consistently remaining in the high octane fuel map, just when I started having fun. I also had misses at idle. Both annoyed the heck out of me. Now with a dirty side catch can, the situation has reversed from the engine running well on "good days", to running well most of the time. Having a cleaner intake and reduced chance of coked rings are great side benefits.
We have a Suburban, and right on schedule at 70K miles (per others' experience on the Internet), I started to get some oil burning despite frequent oil changes. The cause is said to coked piston rings due mostly to the AFM system, but accelerated by crankcase gases.
I love both cars, but manufacturers have limits to what they are willing and able to engineer into their products.