The SBB site might be proposing travel on the S-Bahn trains instead of the Bernina Express. These will take longer than the Bernina Express as they stop at all (or at least a good number of stops depending on the schedule). Although, other than the reservation fee, the price should be the same for a regular ticket from Tirano-Chur.

A DB super-saver fare will likely lock you into certain trains. Unless you book a saver fare with SBB, you'll be able to take any train.

I think you can only book a maximum of 60 days ahead on the SBB site, though the RhB site for Tirano-Chur might allow you to book earlier. For normal tickets there really isn't any advantage to booking ahead.

If you travel from Chur-Zürich, avoid the Regio-Express(RE) trains. They stop a more stops, so are slower. They are shiny and new, but they're crap to travel in.