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The control between normal and primed axes is I believe under the control of the microcode, not the cards themselves (refer to Bromley's details analysis). One of the masterful aspects of the later AE designs were the multiple communicating state machines on separate barrels which managed the ingress, egress, and mill axes. Se particularly the pipelined multiple add/subtract operation.
Regarding the format of variable cards and „address decoding“, Babbage tried different schemes at different times, ranging from binary encoding to „one hot“, or even „n hot“. For instance there is a place where he counts the number of holes needed for a store of some size (1000 variables I think), and it clearly indicates binary code. On the other hand, in one of the letters to Ada when she was working on the notes he explains how it's possible for value from the mill to be transferred simultaneously to multiple store locations. Since it's simultaneous, it must be under the control of a single card. That is possible if there are distinct holes for each storage location - just punch several of them, then multiple columns will be raised simultaneously to receive the value. He also comments that obviously, the inverse operation (ie sending multiple columns to the mill simultaneously) is not possible.