Reasons to autogen:
1) All modded content would appear so that people can see mod stuff on the map.
2) Worldspaces that don't have explicit maps will now have some sort of map without extra effort.
3) No need for modders to either include a 'tweaked' map with their mod's features on it, or a third party to create such a map with common mods that may or may not actually be installed by the one using the map. All they'd have to do (if necessary) is put some useful map markers in place so features are properly popped up on the autogenerated map.
4) Special markers -could- be included that translate into features on the map that aren't easy to interpret by a map autogenerator without help.
Reasons NOT to autogen:
1) Prettier. You can't beat a hand generated map for embellishments and polish, with flourishes and minor details.
2) No extra markers needed, because all the features are already on the picture, even if it doesn't include modded features. Modders can create their own maps exactly as they want, after all.
3) Saves time / resources making a map autogenerator that makes a map that isn't horribly ugly, or that labels features in a way that's readable (or at all).
It's not likely they'll have an autogenerated map... but if they could, would you want it? Would you not want it? What do you think? ^^