You could use the English everything in the main metadata columns, including transcriptions. calibre would use that to build its in-library filenames, and save-to-disk as well.
But for display purposes in calibre, use an "Original Japanese/Chinese" custom column with Just What It Says On The Tin. And use a custom column built from other columns to switch between them and display e.g. the "Real Title".
You will probably also need a metadata plugboard to replace the title with the "Real Title" in the metadata of exported books.
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