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No, I don't think it does.
Maybe you have created a footprint which includes both connectors in the required relative positions to match up with the Particle Electron board and then made a schematic component for it. I understand why you would want to do that - you can't then accidently move the connectors independently on the PCB. However, because there is no concept of part sub-assy it causes the BOM issue you are looking to solve.
I think the best way is just to place the required two connectors on your PCB then 'lock' them in place. They can't be moved accidently and your BOM is correct.