Can think of only one case ... and it's got some catch 22's .... testing/verifying a plugin install/upgrade would not require moodledata/filedir. Once the site stood up one would have to make sure they did nothing involving files uploaded for content etc..
The only time I've done this is when I had no other place to do it. :\
Not recommended unless one knows what NOT to do. ;)
'spirit of sharing', Ken