I regret that I cannot explain your particular case but instead offer my own experience of a Golf. The seller made a mention of the battery being a good one but I thought he was being untruthful because it would be flat if the car was left more than 3 or 4 days unused (and everything switched off). that being my assumption I bought a new battery but the same happened straight away. I did what you have done: I pulled fuses out one by one and also relays. I ended up testing when everything was pulled out. The same result, the battery still went flat and I felt stumped.
I took the car to a garage, the guy asked me to bring both batteries in - fortunately I had not dumped the old one which turned out to be fine. He kept the car for five days and when I returned he pointed to both batteries and said they were duds, he could provide me with a new one. I said thanks but no thanks. Something was draining the battery/batteries. I resorted to disconnecting the battery once stopped for anything more than overnight and kept pondering and prodding.
There was a wire connected directly to the battery at the clamp and feeling I had nothing to lose I disconnected it, it looked almost as if it was a post-production fit. Since then the battery has not lost charge when the car has been out of use for a few days - in fact the original battery lasted me seven years, not long replaced. I have no idea what that wire was for and everything seems to work normally, although I do not use the factory fitted alarm which I think never worked anyway.
There are those who point to two things in particular that are likely to cause problems like the one you have. One is a radio with pre-set circuitry, etc. which needs a fair amount of electricity to stay set, The other is an alarm. Finally, some suggest that mobile phone add-ons can drain batteries. I am not qualified to comment on this speculation/knowledge. I hope you succeed in solving the mystery - these are very frustrating.