I put your mods in my already existing world with over 30 hours delved in, and when generating new terrain, I found tons of enemy bases that were bigger than base, and they were everywhere.
Screenshots: http://steamcommunity.com/sharedfiles/filedetails/?id=737742234

Why are they this big and rich? I'm unable to explore new land with these mods installed because the bases are EVERYWHERE!
Anyway, is there any way to drastically tone down the difficulty of this mod, specifically the size and richness of the enemy bases?

During game setup you can set the size of bases. Can't really control that once the game has started. Remember this mod is intended to make the game much harder. So you'll have move bases and enemies.