Yes, it involves putting the ECU into bootmode - this isnt hard, especially on the bench.
Having immo switched on does make bench flashing a bit harder (Nef needs the immo to authorize access before you can flash over ODB - most bench rigs dont have cluster or pickup ring, so you would need to immo-off if you wanted to bench flash using nef, alternatively you can just flash it in the car).
that's interesting about the keys -- i thought those were matched to the cluster, and as long as you adapt the ECU to the cluster, then the keys would work.
I think you are correct for an immo2 system, but not for immo3.
The problem is that with immo3, you have a 7-byte cluster code, which is passed from the ECU to the cluster when the cluster is adapted to the ECU. This code is then embedded in the keys when they are paired. This means that for a given ecu, only virgin keys, or keys that have previously been paired with that ECU can be paired to it.
You can work around this
Either immo-off one of your ECUs (my approach), so you can easily write it on the bench, and so it just works in the car (and the immo light doesnt flash on the cluster, because the key is authenticated with the cluster).
Alternatively, clone the data out of your eeprom, into your new ECU.
The only complication is that your current ECU is APR chipped, make sure you read up on them before you start trying to read/write this ecu as there may be some complications. I think the general advice is to back up the eeprom on the APR ecu before you try and connect to it with nefmoto, otherwise even reading it can kill your APR tune.
If you didnt want to touch the APR ecu at all, if you can read a dump from the cluster (using vag comander or vag eeprom tool) then you can extract enough info from it to write into your used 032PL ECU so it will work with the immo and start the car.