Hi Claudia and Greetings from Sunny Southern California!
Yes, GL does play "Bobby McGee" in standard tuning, capoed on the second fret. Had to drag out my songbook of "If You Could Read My Mind" to confirm the tuning. FYI - on the 'D' chord he plays the F# bass note on the low E string. Frankly, I'm not quite sure how he plays the bass line as I can't seem to replicate it. Which is why I won't be quitting my day job!
The great thing about Travis picking is it allows for variation and experimentation.
Since Cathy Cowette is apparently still having PC problems, you might want to post your inquiry re this song on the Newsgroup site. There are some serious musicians that post regularly there. I'm a rank amateur but I have fun playing and singing Lightfoot tunes and that's "good enough for me."
Have fun and keep practicing!
John