GCodeClean hits v1.0.2 
This release ‘kind of’ adds the file pre-scan from the road map above.
What I did in the end was to split the processing into 3 phases, with the first phase leaving the GCode in a position where it could be reliably ‘scanned’ to get the length units (inches or millimeters). And with that the code can then constrain the tolerance and clamping values.