There's actually Garlean strongholds in every region of Eorzea - it's why it's stated that Eorzea pretty much is in a state of cold war at the moment, they're literally waiting for the Empire to renew hostilities and launch a full-scale assault on the citystates. As for Ishgard, I remember hearing that they apparently have a neutrality treaty with the Empire, which would explain their 'closed border' policy.