... I did not properly purge the air from the system using Vagcom.
3. In the 6 wks since the engine overheated, it has worked perfectly. I haven’t added any coolant, or experienced any drop in level at the bottle....
I didn't do the prescribed procedure for bleeding either and don't plan to do it. It sounds to me that it is german analism for the existence of that procedure, why?
When you change the water pump, only the block and reservoir are affected, that is (in this new design) a closed system. If you don't disconnect anything else that carries coolant, but the water pump, and refill the reservoir when you are done, there should be no air ingested anywhere else!
That closed loop WP/block, is vented via the reservoir which is using gravity and the WP action to purge air, hence it should be self purging. Now if you disconnect the radiator trying to drain coolant before disconnecting the WP (to make less of a mess), then you would have to perform the VW mandated purging procedure.
A personal story (single data point): with my mk4 wagon BEW engine, I did experience what I now think was a head gasket snafu. I was driving at highway speed and suddenly get a CEL and perhaps some other warning lights, this was probably back in 2008 or 2009, my car is 2004 and at that time it only had perhaps 80k km.
Anyway, car drives fine I pull over into a rest area a couple of km away, open the hood, no VCDS, seemed that there was a tiny bit of oil or soot that passed into the coolant, I could see a black ring inside the bottle that wasn't there before. A little coolant was missing, perhaps half a litre, top off with water. Engine seemed somewhat on the warm side of the range. Waited a little until it cooled off and continued my trip....
For the next probably 2 months and then sporadically, I tried to make sense of what happened that day. To this day I have no explanation, CEL cleared on it's own same day or the following, and I still have the car now with 420k km....drive more, worry less, as I've seen been quoted by someone else in this forum!