Upgrading any of A3's flights departing the UK will incur GBP 13 in additional Air Passenger Duty, as the rate is £13 for economy and £26 for business. Flights into the UK are not charged this tax.

A3 sends the money to the UK government, they don't keep it.

If you merely transit the UK on a single ticket the tax is not payable at all, but I don't think A3 would issue any tickets like this that can be upgraded.