Welcome to the rather complicated world of international train travel in Europe.
You are of course right, that you should not assume that you will catch the 13:35 train. Having only 50 minutes from the scheduled landing and to go through immigration, pick up your luggage and get over to the train station is not completely unrealistic, but not something I would count on.
You can get cheaper tickets if you buy a saver fare for a fixed departure in advance, but this would not be valid for the next connection if you miss the intended departure because of a delayed flight.
You can, at least in principle, buy ticket for long distance trains, also for some international connections, at the ticket machines at the airport. For the connection you are planning, DB will sell you tickets online, so there is no reason to assume that you can't buy that ticket from the ticket machine at the airport as well. So far so good, but now strange things are starting to happen. If you are travelling e.g. the coming Saturday, the next feasible connection is with a departure 14:35, but DB is not able to sell you a ticket online for this connection and I would not be sure if they can do so from a ticket machine or if you are not required to visit a 'real' ticket office.
A further problem is also, that if you buy a flexible (not fixed to a specific departure) ticket for the 13:35 departure, it will, although not obvious, not be valid for the 14:35 departure. The problem is easier to explain if we look at the type of trains used by each connection:
German train tickets come in three categories and price levels:
- local and regional trains (common train numbers start with S, R, RB or RE)
- regular long distance trains (IC, EC)
- high speed trains (ICE, ECE, RJ)
You can use a flexible ticket for a better train category in a lower category train, but not the other way around.
As you can see based on the trains used on your intended itinerary, even a flexible ticket can be used:
- only on local/regional trains between Munich Airport and Munich Ost
- on any train (ticket is for a high speed RJ) between Munich Ost and Innsbruck
- only on local/regional trains between Innsbruck and Ponte Gardena
On the next departure (14:35) you will be taking a long distance train (EC89) from Munich Ost to Brixen. Even if your RJ ticket (Munich Ost - Innsbruck) is valid on the EC89 train, the tickets for the S3 and R17249 would not be valid on the EC89 between Innsbruck and Brixen.
Even if you can't buy a through ticket for the 14:35 departure online and I assume not on the ticket machines at the airport, I would still recommend you to wait buying a ticket until you are sure which departure you are able to catch. For the 14:35 departure, the problem seems to be the last regional train from Brixen to Ponte Gardena. You should be able to buy a ticket from Munich Airport to Brixen and then you can get a ticket for the last bit from a ticket machine at the station in Brixen.
Be also aware, that if you are travelling one of the next weekends, there are extensive construction works at the local train lines between Munich Airport and the city. I would not be surprised if you are delayed and if possible, I would suggest that you take the first possible train from the airport into the city and plan for a longer transfer there to have a buffer for any possible delay.
