Bill,
If you go to the RV-12 VAF Forum that I mentioned in my previous post, you'll see a sticky thread where people discuss modifications to their RV-12s.
I've been following progress of the RV-12 for the last 3 yrs. Like you, I was surprised that modifications can be made. Prior to certification, you have to build exactly per the plan, even having to buy the Garmin GPS from Vans although you might have one already. But after certification, everything is fair game to mods.