When looking at the klayout DRC I see that there is difference made between aluminum and copper back-end. Which flow is used for the shuttle ?

There is no copper back-end in sky130 (apart from the RDL layer, but that's a different vendor). The copper back-end is mentioned in the rule set which is derived from earlier versions of the process, but the copper back-end support was dropped for the current definition of sky130.

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