The internal level's a bit weird. I actually never thought to store it as a signed byte. As an unsigned byte, -1 should be showing as 255. I have always seen a 0 on Jakob and Felicia, though, so something must be converting them to 0 before any chance to save occurs.
If you change a promoted unit to a special class ingame, then open the save in FEFTwiddler, their internal level will appear to be 236 plus their old internal level if I remember correctly. For example, in one of my saves, I changed Camilla from Malig Knight to Witch. Her internal level is 251 (as shown in FEFTwiddler). Her old internal level was 15. It still seems a little off to me; I would expect it to be one lower so that an internal level of 20 gets translated to 255. It's not something I put much testing into, though. I just put whatever's in the save, and figure that anyone willing to modify it knows what they're looking to do.
It has no use currently. I might remove it in the next release, come to think of it. There is stuff I would like to put in there, though, but I haven't really had a lot of time to dedicate to FEFTwiddler lately.
The kind of stuff that I pictured having in there is stuff to rewind game progress (in case you want to resume from a particular story chapter or replay a paralogue) and a randomizer. All of this is partially coded already, but not to the degree I'd want it before letting you all have at it.