Just a quick update, Atmel outlines the trim process in this document - They describe a one time calibration process where they do a binary search using a 32khz reference signal to get the correct OSCCAL - then write it into a byte on a EEPROM to use later.
Using the above document, it might (as I suspected) be possible to do this in real time, so that as temperature changes, the clock speed is updated.
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