You have to understand how train travel in this part of the world works. It is not like air travel. It is mass transit. More like taking a commuter railway in the US.
In order to travel you need a ticket. A ticket is just a receipt that you have paid to be allowed to take trains on a particular route. A standard ticket from Basel to Munich (via either route) allows you to take any trains on that route for the time your ticket is valid (for international tickets that is 2 days I believe).
Such tickets are available in unlimited supply. They never sell out.
The railways also sell discounted tickets. They come with restrictions. For example, a discounted ticket for Basel - Zurich - Munich will have the train number of a particular Zurich - Munich train on it. So you must take that train on that part of your trip, or your ticket is not valid, but from Basel to Zurich you can still take any train (there are six per hour...)
Now with such a ticket, if you were to miss your connection due to a delay on your incoming train (rare in Switzerland) you can just travel with the next available train, and you do not need do do anything at all but find that train and get on.
A ticket does not guarantee a seat. It is perfectly possible that more people board a train then there are seats on a train. So in that case some people will have to stand. And if you do not want to risk that, you get a reservation. That gives you exclusive use of a seat.