Yes the renaming on the hard disk inside the calibre library area is automatic.
However if you now sent the file to the reader using the "save to disc" option rather than "send to device" although the filname might be correct the embedded metadata will still be wrong. Since most readers display the author/title from the embedded metadata rather than the filename you would see some oddities. This would not occur if you use "Send to Device" as as part of that transfer the embedded metadata is updated.
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