You should have a look at gulp-rename
Pretty much:
gulp.src('./*/less/*.less')
.pipe(less())
.pipe(rename(function(path){
// Do something / modify the path here
}))
.pipe(gulp.dest('./finalRootDestination'))
You leave gulp.dest pointing at your final output dir, but modify on the fly the individual file paths based on whatever logic you want inside the callback to gulp-rename.