I've done both, and in my moderate (especially compared to anthony) experience I was much more satisfied with the rock that I put a 4 to 6 hour light cycle on as long I was really careful to clean anything off that was dead or looked like it would die before I put it in the "cooker".
I only say this because I am a huge fan of the surprises that come in on fresh live rock and if I can help them out, why not.
Definitely much easier to just do it in the dark and I can't imagine the curing process would offer more bacteria either way.
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