I thought that the larger aetheryte crystals were a natural occurrence on hydaelyn and that cities were built on or near them on purpose? Much like real settlements developed near rivers or bodies of clean water in reality.
The reasoning was the ease of transportation once the magic to use them as such was discovered. Now, they could get away with them being in garlemald cities by having them use magitek to somehow suction off their natural energies to power other mechanical parts of the city. Heating, cooling, lighting, etc. Then we sneak on in there and instead use it to warp around. Think of a city like Midgard using mako energy.
While, yes, it would pose a potential security risk, remember we as the warrior of light can use that teleportation much easier because of our innately massive reservoirs of aether due to the blessing of light. But almost the whole world's population don't have that option, instead requiring massive amounts of shards to use up, as in the summoning of a primal, in order to move something the size of an army so far instantly. Its why normally armies walking into each other's city via the aetherytes isn't a real military tactic in Eorzean history.
The enclave has a small amount of fighters and had to worry because all it would theoretically take would be an equally small amount of trained, and well equipped non garlean soldiers to have attacked it, hence they're breaking of said aetheryte.
Not to mention, youd have to sneak the entire army in the first place to attune themselves one by one before the second step could even be considered.
Christ I'm a nerd..... -_-