Hi, Ian:

I'll frustrate your expectations by answering first.

I wonder whether the Do Not Remove Rests under the Setup/Transcription options might do what you wish: force Composer to transcribe as performed. Or at least much closer.

That would mean change the setting in Transcription Options, then choose Retranscribe ("qrt") under the Format menu.

Not sure about the "duration/separation" value you mention, unless it's as above.

Good luck.

David