I kind of have the same question.. I want to fit custom exhaust cans (haven't done any filter adjustments yet) and asked a mechanic if this will cause my bike to run lean. He said it won't do much harm and will probably operate fine.
On this forum i read various stories regarding his topic. I'm quite confused on what to believe now.

You said you burned a hole in your piston before.. on what bike did this happen? XT engines are a lot more bulletproof than most other singles though..