I've had a lot of fun customizing my dungeons underground, particularly making some awesome looking bunkers. However, the medieval tower that spawns on the surface would look real cool if I could change it as well.

Give you an idea of what I've done with your dungeons: http://i.imgur.com/ZZsIkQt.png

First of all, glad you're having fun!

You can change the tower. It has its own tower type and theme property.

"tower" : {
"type" : "ROGUE",
"theme" : (a theme definition similar to how level themes are defined}
}

available towers at the moment are:
ROGUE, ENIKO, ETHO, PYRAMID, JUNGLE, WITCH, HOUSE

the etho tower (as in ethoslab) is death games. the eniko tower is the one you'll usually see in mountain areas.

That is awesome! Thank you so much for the mod and response!