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Copy-in rather than copy-out in transpiler (#11176) (#11182)

This shifts the deepcopy of instructions in the transpiler to be at the
input stage, rather than the output stage.  This more closely matches
our behaviour before the passmanager refactoring, but also has a
performance benefit for circuits that require significant routing and is
typically safer for transpiler passes.  Output circuits are typically
larger than input ones, so copy-in means less copying, and also makes
the ownership model for tranpsiler passes clearer: a pass can assume the
input operations are entirely owned by the circuit it receives, and that
a pass must output a circuit that entirely owns its operations.

(cherry picked from commit eca34781d)

Co-authored-by: Jake Lishman <jake.lishman@ibm.com>

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