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The level 3 preset passmanager by default runs 2q block collection which is then synthesized into a unitary. As long as we're running that in the pass manager it's not really possible right now to preserve input unitaries through the transpilation. A potential follow on PR could potential skip the synthesis pass if 'unitary' is in the basis so the optimization pass would just collect 2q blocks into a unitary and pass that to the backend directly. However, that's not in scope for this PR (and it's not clear if we want that or not).
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