I have fitted and mapped aftermarket ECU systems on everything from a Corsa to a Skyline but never a MK5 Golf.
The ME9 ECU system that is fitted as standard is a very very good ECU and extremely flexible and has many benefits over an aftermarket system. An aftermarket ECU system is only really required once the original system is no longer capable of delivering the desired results.
The AMD/Milltek car will probably have an aftermarket ECU, I should have asked when I was with them at Croft.