Originally posted by retsam1:

2. There are various explanations concerning how caves not spawning in is an intentional by product of allowing you to still play a map after an update changes it significantly.

That's not been a good reason for a while now, given there's a mod to selectively repopulate regions of the map with tar pits, mountain caves, etc. The Mistlands update would be a really good time to add that feature to the core game.