Interested in what you say about iBackupBot. I tried it today, and it could read the backup files just fine, but I couldn't see my device in the left-hand pane of the explorer window. Would like to use this to do a clean install and then copy back my iMessage database and attachments.
My device data got corrupted somehow, so I had to do a fresh restore. I was going to just back up the messages and attachments the traditional way, until I discovered a blogpost somewhere with a great solution to my problem. Here's what I did:
1) Made an iTunes backup of my device with the messages and attachments I want to keep.
2) Used iExplorer to export the message and attachment data in HomeDomain and MediaDomain to my Desktop (I think those are what they're called). You can probably do this step with iBackupBot but I wasn't planning on using it at first. I realized iExplorer can't write to a backup, it can only extract things, so I had to switch programs.
3) I reset my device to factory settings.
4) I made a clean backup of the newly-restored phone, and used iBackupBot to paste the message database and attachments into the clean backup.
5) Used iTunes to restore the "tweaked" backup to the phone.
Voila, it worked like magic. All of my messages and their attachments were there, back to 2011 when I got my first iPhone. I didn't have to directly access my device from iBackupBot at all.