The underground mining structure being different is fine; I hope it's not much more expensive then the surface one.
![Wink ;-)](./images/smilies/icon_e_wink.gif)
After unlocking scanning, it should unlock more normal ores all over the map, as well as the new deep ores; that way, we can reuse the same close areas to our base later in the game, after we've already exhausted the normal ores there.
![Smile :-)](./images/smilies/icon_e_smile.gif)