Is there any way to add RID's to the hard disk on the computer using riorid.jar?

Not at the current time. It only writes to the player databases, not to the tags on the files themselves.

What is the benefit for the Central to have these in the comment field

Because of a limitation in the code of the Central that prevents the creation of the "RID" field in the Central's database, the comment field is the only remaining field in which he can put the data in that particular case.

is it there just for the riorbackup.jar to use to know where to place the file into the correct playlists?

It's there for whenever Jemplode or Riobackup needs to find out if a file is a duplicate, or to definitively identify/locate a specific song regardless of how it's tagged.

Example 1:
- I run Jemplode.
- In Jemplode I open the Central and then also open the Empeg.
- I copy playlists back and forth between the two devices.
- Rids are used to decide whether just the playlist entry needs to be copied, or if it needs to copy the song file, too.

Example 2:
- I have all the song files on both devices.
- I back up all the playlists from one device.
- I restore the playlists onto the other device.
- Rids are used to match up which songs go with which playlist entry.

Also, does jEmplode place the RID in the comment field on the empeg's files so you do not have to rerun riorid.jar each time you add music?

No, the music files and their tags are not touched. Remember, we are only working with the player databases, not the MP3 files or their tags.