We have a system in place that can manage the snapshots. The reason to have a base_path is so we can move the snapshot to glacier as per this question Is it possible to move a one time snapshot to Glacier?
Which should be ok to do providing we don't alter the files on that path. The easiest way to seperate this is to have a repository per index. Providing that there aren't any limits on the number of repositories and the snapshot api continues to work in the same way.