AFAICS xprop is able to read multiple values for an atom property (separating them in output using ',') but is unable to set multiple values. Could you considering adding such a feature as it was requested by user ?
A fairly common use case for this is trying to set WM_CLASS (which is a struct of name + class; the class is the important one but xprop can currently only set the name).
on Dec 07, 2016 at 14:24:00.
(provided by the Example extension).