I just thought of something: My suggestion that the re-creation of the Enterprise was underground, overlooks the fact that why didn't the Gideonites themselves start moving underground?
That reminds me of something: When Spock is speaking with Hodin and he mentions the possibility of Kirk having materialized somewhere else, Hodin say "I hope it was on dry ground". This might suggested that Gideon was very extensively covered by oceans and lakes. This could've served to vastly reduce the amount of habitable land for people. Also its possible that on Gideon they drastically restrict the amount of land people can actually live on and preserve certain lands for food production. After all they have to feed their people and all the Gideonites we see seem to be well fed and robust.