the answer to my own question from february is yes, jam does allow you to specify different indices.
to set index 0, choose preferences from the edit menu and enter the value you want in the "default pause for new tracks" box. add a track and double click it. change "silent pause" to "audio starts in pause." the track now "starts" at index 1 unless you scan backwards to index 0. useful for making a hidden track before the first song on a disc.
-r.