Sea Tunnels are in the BUG options under the Caveman2Cosmos screen, far right at the bottom. You may need to scroll down to see it. Latest SVN, I just checked. There may still be the problem that you have to turn the option on to show obsolete/unavailable worker actions to actually get the button. A save game showing that issue would be useful. If you have one please post it in the bug thread for me to look at. I prefer City Limits and thought they were still in there and scaled to map size and game speed. However I may be playing on the default of both and so I would not see what you are reporting. personally I would prefer much harder limits similar to the one we have before Tribalism.