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scancode-toolkit happens to contain a good number of data files (~ 68K)
What I did as a proof was to:
unzip the built app
remove enough files to go below the 65K limit
rezip and run the app... and things work fine
Since shiv depends on the boostrapping mechanisms of Python zip importer, this is dependent on @thatch Zip64 support in import being merged in python/cpython#94146 ... therefore I am not sure that there is anything to do here beyond some documentation.