Finally, I managed to replace my ME7.1 with a used one without boot mode. No benchtop setup, no soldering, just swapping it in the car and programming through OBD. I own a 2001 A6 4B with AML engine and I used a cheap "AutoDia K409" interface from ebay.

First, I read the EEPROM of my original ECU. I tried different versions of VAG EEPROM Programmer as well as CAN Commander, none of it worked for me. The only tool that could read my EEPROM in OBD mode was ArgDub's me7_95040 version 1.3 (while version 1.31 always stopped after some reading and version 1.4 never even started to read):
http://nefariousmotorsports.com/forum/index.php?topic=1168.msg11101#msg11101

Then, I extracted the four digit login code from the saved binary file using VAG ECU EEPROM Calculator v1, found it here:
https://mega.nz/#!1N1RzQDJ!0v_JpryEr8ctiTcZ5InVmuQKKA8fabXjKhu1aVNoXpA

After swapping the ECU in my car, I repeated the procedure to obtain the login code of the replacement one.

Using the original and replacement login codes (here called PINs) I linked ECU and IMMO following the standard procedure in VCDS:
http://wiki.ross-tech.com/wiki/index.php/Immobilizer_III_ECU_Swapping#Engine_Control_Unit_.28ECU.29_Swapping_.28USED_ECU.29