For that reason most people use the tag field ALBUMARTIST with the value Various or VA for compilations. Another option would be to have a field called COMPILATION with the value 1 for compilation and 0 or nothing for regular artist albums (itunes does so). The first method has the advantage that you can also use artist names for dj-sets, cover albums or simmilar things.
you can use:
%genre%\%albumartist%\%_directory%
if all your album have an ALBUMARTIST field.
or:
%genre%$if2(%albumartist%,%artist%)\%_directory%
if only the compilations have an ALBUMARTIST field.
or:
%genre%$if($eql(%compilation%,1),VA,%artist%)\%_directory%
if you don't want to use an ALBUMARTIST and want to use the iTunes typical compilation marker instead.
EDIT:
i've read you request again, and this is also possible.
"exception rule so that all folders beginning "VA-" are put into genre/VA/foldername":
%genre%$if($eql($left(%_directory%,3),VA-),VA,%artist%)\%_directory%
this is only based on the first three characters of the foldername without a need to add new tag fields.