I've had my SAFC2 tuned on the car and yes, my battery has been disconnected whilst performing other mods. The SAFC2 has it's own internal memory which retains the tune.
As for the parasite thing, I'm not sure... I read somewhere that the ECU is a "learning" computer so you might be onto something
Nonetheless, this upgrade is due to happen in a few weeks... if I don't find anything reliable, I'll just wind down the boost level and have my tuner go at it with SAFC2 alone.
Once something good pops up, I'll just change things around~