Pro sites and disk quota limitation


I plan to activate the pro site plugin on my WP network in the near future and I have a question about the disk quota limit options.

Some plugins (for instance: NextGen Gallery) are not using the /wp-content/uploads/sites/<blogID>/ folder to store their data but still use the former /wp-content/blogs.dir/<blogID>/ folder or even their own folder in /wp-content/ (like for instance Flagallery which uses a /wp-content/flagallery/ folder).

So I wonder if the data stored in such "unofficial" folders are taken into account in the disk usage quota ?

And if not, what would be the trick for an homemade plugin to add these unofficial folders into the disk usage calculation ?