Create any new score with any anacrustic (‘pick up’) measure.
If the first measure is incomplete, count from 0, or take 1 off all the measure numbers.
Versions 2 and 3 both count anacrustic (‘pick up’) measures from ‘1’ (i.e. not 0), while the musical convention is to count them as ‘0’. The docs at MuseScore.com suggest that ‘an "irregular" measure is not counted in the measure numbering’ and that ‘Normally a pickup measure is marked as "irregular”, but that doesn’t seem to be the case.
MuseScore has the option to ‘Exclude from measure count’ manually, though I doubt that you’ll consider that an adequate solution.