Can you provide a reference for this claim? It is surprising to me. My understanding was most variegations are from random genetic changes. According to
wiki there ARE some virus-linked variegations, but I don't think this is the norm.
Whatever.
But one of the issues is that quite often some branches, not all of them, revert to a non-variegated form. It's not a problem for landscape trees because you can cut off the branch (when the tree is reasonably small), otherwise it is usually stronger than the variegated form, and after a couple of years, the whole tree can lose its variegation. There are good examples of that in a neighbouring street planted with high-grafted Acer negundo: they were originally variegated (like A. negundo 'Flamingo'), but most of them have at least half their leaves turned back to green.
For bonsai it's an issue since if you built a balanced tree and have to cut a branch which is necessary to the design, it might mean years of work to be binned.
Anyway, the variegation on the leaves distracts the eye from the shape of the leaf pads.
Also, on maples for instance, very often variegated leaves are distorted, not very consistant with an overall shape.
For instance, pics from a healthy 'Gwen's Rose Delight' (aka 'Shirazz') at different stages throughout the season. Very nice patio/landscape tree, no good for bonsai IMO:
April:
May:
September: