1 - Are you saying ripping out the coiled wire to the Z motor will cause it to not work properly?
2 - Are you saying rewriting the Z (and maybe X/Y) motors will cause them to not work properly?
When you say “cross” – you are not specific or detailed. Is there some sort of impedance or EMI issue you are correcting that can be inadvertently undone by introducing a custom drag chain?
After just experiencing this last night, while wiring up my other controller, I think basically what they’re saying is - don’t trust the color codes on the wires, as they don’t match those coming off the motor (if you look at the motor reference specs).
In the end, it’s all quite easy to fix, if you do goof, simply swap any pair of coil wires. You can check which pairs of wires are in the same coil with an ohm meter. Any two wires that have a measurable resistance across them - belong to the same pair. When wiring up, if the motor moves in the wrong direction, simply swap any pair of wires to reverse the direction.