Hi Jerome,
we are testing this issue with PayPal payment method (fixed price of 0,35€ + 3.4%), but I want to do other tests later also with other payment methods.
As you can see in the attached file that reports the order screenshot (but it's the same in the checkout process), the VAT amount is wrong.
All the prices are including VAT, also PayPal price is with VAT. I know that there is no tax category option in payment method but it seems that the payment amount is correctly calculated including VAT: 13,45€ (11,03€ + 2,42€ of VAT).
Now if you calculate the correct total VAT, you'll find that the correct total VAT is 71,92€ meanwhile the value actually reported in the order is 69,50€
The difference between 71,92€ and 69,50€ is exactly 2,42€ of VAT, that's why I suppose that in the total amount of VAT of the order the VAT of the payment method (2,42€) is not added to total order VAT.