If the leasing agreement covers/includes all servicing then ask them about that, if you are paying all the servicing bills then you have done the correct thing.
I think that the back ground to all this is:- it is well known that all car HVAC systems lose a small amount of the refrigerant charge each year, it gets lost across the seals and the flexible pipes, so after some time the system will start to underperform and so need "topping up" - the only way to do that while it has a greenhouse gas in the system (R134A), is to recover all the remaining gas and weigh it, place the empty system under vacuum to make sure that it is dry and to make sure that it is still what goes for "leak free" then back fill that system with its specified weight of R134A and maybe a drop of lubricating oil. At the same time, it is generally good practise to sanitise the system by setting off a "bomb" in the passenger compartment and running the AC on recirculate, ie to kill off any bugs that have been growing in the wet/moist evaporator areas.
Now, as far as I know, running an AC system while it is slightly under charged will not damage any part of it, ultimately you will find that the chiller is not working as well as expected, if the refrigerant charge level drops too low, the system is designed to protect itself and fail to operate on a high duty cycle. There may be an issue with an under charged system causing you to waste fuel, but I'd doubt if you would notice that or be able to put it down to an under charged AC system. These systems are designed to be "critically charged" all that means is that for it to work perfectly there is only a small tolerance on the acceptable refrigerant charge weight, though how well it works at a lower or higher charge weigh depends on the ambient temperature.
As you have found, VW Group advise all their workshops to give an amber warning on AC and wiper blades every 2 years, as far as the AC system is concerned, I'd not think that any testing/checking the performance has taken place, other than that car is now at the 2 year mark! I have had it with my wife's 2015 Polo and I said "no" though I have checked the system performance and set off a antibacterial "bomb" in the car (bought from ECP for very little money) - but that was to supposedly protect our health.
