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A Canadian 'ex-pat' friend says that 'at the end of the day' is from keeping accounts . Small businesses such as corner shops,'cashed up' and balanced their books daily, at the end of the day. They would then know the day's takings and spot any unexplained shortfall immediately. The phrase means, ';when everything is taken into account' .
If so, the phrase must be much older than 40 years but its figurative use may be recent.That seems unlikely, as you suggest QM