Amdapor keep has zones too. So does Halatali.
Uhm, no they don't have zone lines. Teleports are not zone lines. You can't see things on one side of a zone line from the other. In these dungeons you can see the stuff in the areas you're visiting or came from. Look down from the balcony in Ampadoor. You're still in the same zone.

Only Pharos Sirius and CT are broken up into multiple zones.

On CT it's probably for serverside performance reasons (It's easily the largest dungeon in terms of physical area covered) because it's one world as far as level design is concerned; it's just like the main cities, they're split into 2 areas for serverside performance reasons (except Gridania which was significantly redesigned for 2.0)

For Pharos Sirius, it's probably because the dungeon is most likely an impossible space (meaning, different floors would have to clip into eachother for it to be one zone).