I think this is more of a historical artifact rather than a fundamental measurement. In the Millikan oil drop experiment he was able to measure quantized units of charge by stripping a single electron from a drop [1], so much later when quarks are figured out they are proportional to the base unit of charge.

This is similar to how Ben Franklin, having no knowledge of elementary particles, defined the positive and negative polarity of electricity, so we have "electron holes" flowing from the positive end of a battery to the negative end in "conventional current." [2]

Edit to add: the electron's non-even charge numbers comes into light when you see that the charge is 1.602176634×10−19 Coulombs, where 1C/second= 1 ampere. If we were trying to come up with the definition of an ampere with nice base 10 numbers of electrons this would be much different.

[1] https://en.m.wikipedia.org/wiki/Oil_drop_experiment

[2] https://eng.libretexts.org/Bookshelves/Electrical_Engineerin...

There exist "stable" exotic particles of that have non ordinary amounts of lower level quarks. https://www.symmetrymagazine.org/article/lhcb-discovers-long...

Maybe they might have non integer charge.