Only case where I can think that charges would be applied is if you’re purchasing from Fairphone directly and shipping to Switzerland. Fairphone will not charge VAT in those cases, but swiss customs will. The bill for this, plus a handling fee, is levied by the courier (though the charges come from the swiss government - see here). Examples of approximate prices (they will vary according to EUR-CHF exchange rate) for this have previously been posted e.g. here.
P.S. I hope Fairphone support get back to you soon - unfortunately there isn’t a lot of Fairphone staff on the community forum, so other than trying to figure out what may be going on there isn’t much that can be done here.