I have a 99 986 and I am sure the 6.x durametrics software will work with it. Mine was on when I bought the car. I assumed the temp display was normally on and didn't even realize there was an optional stalk that I was missing. I clicked the "turn on OBC button" in the durametrics software and it returned an error that the OBC was already on of course. Based on that I'm pretty sure that it's sending the right command to the right location in memory.
I think you should be safe turning it on. I won't vouch for the rest of the 6.0 software though. It's definitely still in beta.
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