It seems a bit hit and miss TBH.
I broke a 2.8 Quattro last year, and only having one key for my own car, decided to use the 2.8's key on mine. I got a blade cut, and used vagtacho or VCDS (cant mind which) to program the key using the SKC i extracted previously. My car has immo3, and it all worked fine, reusing the original transponder.
However recently i tried programming a used VW key into a mates bora, and it wouldnt work. Everything looked normal thru the process, but the key simply wouldnt take the coding. Fitted a new transponder and that sorted it.
Perhaps it worked for me because the "used" transponder was from an IMMO2 car?