Thank to Nigel for letting me know that friends of his flew from Madeira via Zurich last week, to get back to the UK, and they were stopped and fined in Zurich.
Although they had 27 printed pages of Covid tests in Madeira and booked ones in UK and all relevant documentation but we’re still fined, as they had pasted their 99 day stay.
Most countries are waving this, and there have been other stories on social media about people being stopped in Zurich, and most have been let on their way.
The fine was 1200 euros or Swiss francs between the two of them, so I would certainly avoid this route now.
Flights are now running from Lisbon to Heathrow, so this is probably a better option now.