If there is no level sensor in the tank, then your car doesn't have coolant level sensing. The header tank is the only free surface in the cooling system so you can't put a level sensor anywhere else.
The only coolant sensor you have is the one you have already changed. It has two sensors in the one housing, one (G2) feeding the dashboard and a separate one (G62) feeding the ECU.
Flash+beeps is the dashboard warning of a coolant
problem. Not necessarily level, just a
problem, a reading out of spec.
If you see no faults with VAG-com, then the ECU must be seeing reliable data. Perhaps VAG-com doesn't test the sensor feeding the dashboard, just the one feeding the ECU?
One thing you might try is cleaning the connector to the sensor unit. Spray with electrical contact cleaner, plug and unplug several times to try to wipe the contact surfaces clean.
Otherwise it might be time for a new sensor assembly - but I'd like to know if VAG-com can detect faults in the G2 sensor, because that's where your faults most likely lie.