At the moment, this is really the only mystery that Alexander has to offer... which is probably why a lot of people are disappointed with him. The Goblins are the primary threat (at the moment), and we know what their goals are. So, there's not enough mystery and intrigue to keep us interested at this point, and the end cutscene of A4 did nothing to warrant a renewed interest in the story like T5 did with Bahamut (most people could not wait to get into the Second Coil after seeing that).

That being said, it is an interesting question. Personally, I'm assuming that the codex is simply an object, and Alexander is the Eikon. Further, I'm also assuming that Alexander is the means to an end for Goblins. He's what their hopes and dreams are riding on (quite literally); however, I don't think they truly know what they have gotten themselves into.

So far, Alexander has mimic'd Bahamut in his implementation. First stage is dormancy. This was the same for Bahamut. He did not speak to us and all of the threats presented to us in the First Coil were of Allagan design. Second Coil showed us a bit of Bahamut's intent. The menacing feeling of the unknown and suspense was replaced with a raising of the stakes and a concentrated will. Bahamut himself became involved. Final Coil was the show down. Basic story structure 101: Introduction -> Rising action -> Conclusion. I think we can look forward to the same design for Alexander. The first stage of Alexander (suspense/tension and mystery) were utterly lack luster by comparison to Bahamut's version, but I'm hoping that the second stage makes up for it with a deeper sense of threat from Alexander himself. As he becomes more complete and aware of what's happening, he stands to pose a much more troubling threat to the immediate infrastructure than Bahamut did.