The Atomic TBI has a MAP (Manifold Absolute Pressure) sensor not a MAF (Mass Air Flow) sensor so the location of the BOV in the hat is OK.
There are only 5 target A/F ratios you get to enter into the system.
Idle, Cruise, WOT, Nitrous and Boost.
You are correct, outside of those 5 fuel control parameters the user has no way of fine tuning the fuel map.
The problem is the Paxton produces a variable boost proportional to engine rpm and the Atomic's ECU only has a single boost parameter to work with so it will only be correct over a short range of boost and rich and lean on either side of that short boost range.
The Holley Super Sniper gives you 4 A/F ratio inputs for boost. 0 PSI, 7 PSI, 14 PSI and 21 PSI
I'm not seeing anything better for the FiTech TBI units.
It would also be possible to use a Multi Port unit that is laptop programmable and adapt it to your Atomic TB.
You have to bypass the ECU in the Atomic TB and wire directly to the injectors and MAP sensor.