In the past During service the VW technician should connect the vehicle to the fixed diagnostic equipment, this connects the vehicle to VW Factory.
During the process All updates available are applied to the vehicle.
the T6.1 has over the air capability, which means some updates are carried out wirelessly. (But appears to be limited)
All updates are applied Directly from the Factory and should be applied for free during service.
VW technicians have no clue on the Software side of things, they will not attempt to fix issues, instead they rely on approved third parties to carry out diagnostics and fix issues, I would suspect that is what the charge is for ; Third party diagnostics such as "SatNav systems Surbiton"
The Head unit is covered under extended warranty and if faulty should be replaced.
The above company can diagnose a potential issue and fix it if required, but it should be fixed under warranty