The ebuild automatically creates a home directory, instead of using /var/empty; for a service, this behavior doesn't seem to be appropriate. I have never, in years of using ProFTPD, found a need for it to have its own /home directory.
That directory is added because it will be the default home for the anonymous ftp acount. If you do not want that just remove it and change the home in /etc/passwd
If the directory is being used by the application, it may be more appropriate to place it in /var, along with the home directories of many other services. /var/ftp would be the obvious choice, as it would match /var/www.
*** Bug 88728 has been marked as a duplicate of this bug. ***
In environments where the the home directories are a networked file system and the local superuser does not have exportable superuser rights this fails and leaves the install in an incomplete state.
This is nolonger an issue with net-ftp/ftpbase
