From a game-mechanics as well as lore-based thought process.... aetherytes are what the player is used to, and there has to be some form of 'warp points' available in any location we visit. Would it be better to maintain that familiar label, or go with a 'local flavour' version and call them magitek transporters even though they do exactly the same thing?

Actually it might be best to stick with aetherytes because of Return. Given the lore explanation of how the spell works, it probably wouldn't make sense to be able to mark a magitek device as your home point instead of a real aetherial beacon.