That’s what the 3D timing map is for. You can lock out the distributor and just use the ignition box to control all your timing, including adding or removing advance based on throttle position and MAP.
The way I read the instructions is you either have to make the box not do anything to the timing or lock the distributor out and let the box run the timing.
I need to read a bit closer but it seems you have the distributor and the box at odds with each other.