have you calibrated the printheads ?

Not sure how you do that on an idex.

with the standard dual nozzles it's very much like an inkjet calibration.
Each ehad prints a series of lines and you pick the ones that line up best.
Then repeat till it's bang on.

I would think there has to be a similiar process with idex machines.

My only issue with flashprint is that there is no place for using starting (or any) gcode. Otherwise you could simply create your own offsets.

There might be something hidden in the firmware that you access via the control panel.

Have you done any two colour prints ?
the traffic cone is a good test print as it's pretty small and quick: https://www.thingiverse.com/thing:21773