In regards to the "#neighbors" being mandatory:
Pros and Cons, Gandalf, which I think you've said before
It is a big con for your random map making, and I'd imagine it'd be pretty annoying for making new maps too. Since they have a Dom1 system that does this mapping, however, hopefully the mapedit tools can include a program to generate the neighbors it would have caught, and output them to a text file? I suppose Dom1 must have that matrix loaded into memory, so potentially just load a game with the file, and then some memory dump spelunking. Or the source code/algorithm/etc so a third party could do it
It's a big pro, however, for any third party map tools. With the neighbors list, you have all you need in the .map file to generate a complete distance matrix! Seperate post for that one coming (might be long)