That's a problem generally encountered by aircraft on a non-EU registration.
And that only when they are actually imported to an EU-country, imported usually being defined as "for longer than six months consecutively", or something to that effect. Aircraft on the Swiss register don't have to pay VAT as soon as they land across the border, but if they are permanently stationed at an airfield across the border (usually either in France or Germany), because flying there is generally cheaper than back in the home country, then either French or German customs might eventually come knocking and with a rather stiff bill.
Ciao,
Dg800