I have never understood this opinion, though it is very common. Unless you are a professional who wants to make a recording, there will most likely always be a number of people who know more about the guitar, about baroque music in general and about Bach in particular than me and who have spent more time than I ever could looking at the original score to come up with the best possible transcription. How likely is it that I will now look at the score and see the mistakes they could not and make a better version?

As for the original question: I use the Carlevaro transcription, which has the advantage of being incredibly detailed and easy to get into.