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According to the FAQ:
Which ticket do I require for international arrivals or departures? Are Swiss Travel System tickets valid on these trains? Are reductions available? Swiss Travel System tickets are valid only on the national route network of the STS. For international arrivals and departures, separate tickets are required. When booking an international ticket to Switzerland, you can (under "Reduction") deduct from the international point-to-point fare that part of your journey covered by the Swiss Travel System ticket in your possession.
Please read the corresponding text in the FAQ under the "traveling to Switzerland" section.
In short: You will get the swiss part of the international ticket for free, but you have to make sure you book it correctly to get the discount. If you do not need to reserve a seat, you can always only book the the tickets outside of Switzerland.