Organise Music and retain m3u, nfo, sfv files etc

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.