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 Sep 27, 2016 at 22:27:25.
(provided by the Example extension).