Hi
@fortview, we made this journey last week. There was a bus substitution between St. Etienne and Le Puy. It was all very straightforward - when you buy your train ticket, you also get a ticket for the bus. The bus leaves from outside the train station and was waiting for us as soon as we walked outside.
One small point - there were two Le Puy buses outside the station. The first one filled up quickly and we were encouraged to get on the one behind (which had a slightly different number). This bus was more comfortable and less crowded BUT it took a longer and more scenic route. It was a beautiful journey, which we really enjoyed. However, if you want to get to Le Puy faster, I'd suggest getting off the train promptly and going straight to the bus queue. We dawdled quite a bit as were weren't in any particular hurry to get to Le Puy.
Bon Chemin!