Daughter board socket issue

I understand that this is a good solution and I would probably go for something similar would I not have the automation already in place…

That would be nice, however it seems to be a quite difficult. The BOM part not so much but the position files. It is easy to create a few procedural lines of code that will do it for one specific case, but creating a universal tool in KiCad to describe the transformations seems to be way more complex.

I dont know any tool that would do what the op asks- generate a complex BoM.
This is a specific case. Suggest generate this as a single component in symbol and footprints.
THis way there wil be no question that the two connectors have registration.
Ensure the fab people have the XY centre pos of the connectors.
In your footprint symbol, place a mech or doco layer that shows the crosshairs of the registration centre of each connector. Have this match the component supply method (likely to be tape and reel). At the crosshairs, show on the drawing (doco layer) what the X,Y offsets are for each connector from the single component origin (where the pick and place file says it is).
If you do this, everyone in the chain knows what to do and you do not need to supply any other information.

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