That's right, with the factory ECU, an S-AFC will only tune for vacuum conditions (idle, cruise etc..) as well as adjust for slightly larger injectors.
You need the FCD to keep the factory ECU from seeing boost because it has no fuel & timing maps for that volume of air, and it cuts you off.
Once you're in boost, the FMU takes over and you are basically tuning by setting the correct fuel pressure relative to boost (not 1:1 like a stock turbo DSM reg).

This is a crude way to tune, but if you don't ask for much it's acceptable!
Standalone is best, but they can cost a lot.