While I like the idea of having expensive long-range transport options like the Djinn, I think the existing scheme is a bit strange. While it makes sense that the Djinn needs to be amphibious, it seems unusual that teleportation as a function is limited to the amhbibious factory- the rest of the units in this factory will also be amphibious. Most likely this means they will not actually need the teleporter the way landlocked units will. I also don't really like the way the Djinn creates a 'beacon' that is not actually a unit. I think the player should be required to construct something to act as the beacon, even if the sum of the cost of the beacon and Djinn matches the price of the present Djinn-only self sufficient teleporter.
I propose a new teleporter structure, which can be morphed into a mobile version (the Djinn) and back again, and reworking the Djinn's teleport system. The structures can be used to teleport units between themselves freely, with infinite range. This is essentially the Djinn's ability now, except you use one of them as the beacon, and a second one as the end point. You can build this structure directly without having an amphibious factory. Also, you can use a Djinn to walk to wherever you wish to teleport, and morph into the stationary structure.
All your teleporters would potentially be able to teleport to any other allied teleporter, creating a robust gate network. A little bit of UI sauce could be created which points one of the teleporters at another teleporter, meaning all you have to do is move units within range of the start point to send them to the end point.
The mobile Djinn could be reworked to have a limited-range "send" or "recall" teleporter, or perhaps even both. This would be useful with a single Djinn, although would have limited range compared to your teleporter network. This also works to increase the dubious mobility of the amphibious factory. Simultaneously, landlocked units still have access the expensive long-range teleportation of the kind they will find more useful.
Because a single Djinn or teleport structure would not be as useful as it is currently, it would need a price drop. You would need two gates to get the same utility as one Djinn presently, so by approximately half, to 800 for either one, seems justified.