It's been a long few days but I believe we've found a solution to move forward on a modification for the existing Just Friends modules that will avoid any issues with potential damage to unprotected module's outputs.
At present we're arranging the logistics of how these modifications can happen seamlessly with as little disruption as possible. Before posting details though I'm awaiting confirmation from Intellijel that the proposed modification will absolutely avoid damage to their Metropolis module (Verbos has already confirmed this works for them). I should have confirmation by the weekend, either direct from Intellijel, or trial by fire at Control.
In the meantime, the patch-connection-order workaround is a safe way to use the RUN jack.