If you can find a copy of the ICAO "Final Report of the Standing Committee on Performance" (cira 1958) you will probably find an explanation. Which would include a lot of probabilty analysis on things like the probability of being at a lower speed than desired for all sorts of reasons. It was a very interesting read on how pretty well all performance related aspects of transport aircraft developed. Of course it didn't include more recent changes such as performance based on Vs 1g and minimum level flight speed (Concorde).
Don't forget that most certification standards require a safe landing from Vref minus some thing - usually 5 knots. I have seen a few light aircraft which cannot comply (at 1.3vso minus x), so Vref ends up being more than 1.3Vso. There may well be transport aircraft with the same situation.
Pity I dumped my ICAO report along with a bunch of AAEE documents during a recent "life decluttering" event!