You always start a train ticket purchase by selecting a schedule. And usually the schedule selected will be printed on the ticket.
But that does not necessarily mean that you are bound to every train on that schedule. If you buy a ticket from Basel to Salzburg only on the Zurich - Salzburg part will you have train binding. And for the Basel - Zurich part you may or may not be offered a reservation, but for that segment it is anyway not needed.
So the best thing is to buy a through ticket, as that gives you the cheapest price. If you then. later find out that the schedule between Basel and Zurich has changed you just travel according to that changed schedule.
Know that when you buy a train ticket the railway must transport you. They cannot at their own discretion cancel it. So if a schedule change makes the original schedule impossible your ticket automatically, without you having to do anything, becomes valid for the changed schedule.
Regarding different prices you see for domestic ticket: SBB sells two kinds of tickets: The first kind are normal, “point to point”. You will notice that these will always be the same price regardless of which train you pick between Basel and Zurich, and irrespective of when you buy the ticket. These were until recently the default. Tickets for a route, not a train. And when buying a ticket you did not even get asked about which train you wanted to take.
The other kinds are supersaver tickets. They are a new thing, and deviate from the norm in being train specific. They are cheaper, but not flexible. They are “tickets for a train”, and are the exception, not the norm.
But anyway, this is train travel. Just buy a ticket Basel - Salzburg on www.oebb.at, and just stop worrying until a couple of days before your trip. Then look up the schedule, and you will see that maybe you do need to lave Basel a few minutes earlier, but that will be it.
The other
