No, I genuinely think it's all unrelated. This sounds weird coming from a massive lore nerd that usually loves everything linking up, but they seem to be deliberately avoiding that particular link as much as possible.
Not only is there no real crossover point between the two stories anyway outside of both being conceptually rooted in 'Alexander the recurring Final Fantasy primal', but the game itself had ample opportunity to have someone bring up the connection to hint it back onto the table, since Y'shtola was actually involved in that storyline. It's a rather easy Chekhov's Gun to put back on the set to remind us, so the fact they didn't feels like a deliberate attempt to avoid us drawing that line. I suspect it's actually also why the game's so deliberately refused to give us an easy look at Alexandria Castle, either by deliberately directing attention away from it in the Alexandria dungeon, or only showing it in essentially caricature in Yesterland; it's such a natural and obvious money shot that I feel like they have to be deliberately avoiding it, to let the story of Alexandria build itself up without distracting us with 'hey, that's just Alexander'.
And that's all putting aside that 'Alexander the recurring Final Fantasy primal' is itself a complete nightmare, because every game that bigs it up uses it differently, to the point where it'd be genuinely hard to reference both at once. In FFIX, Alexander was essentially the protector deity for the city of Alexandria, which is a completely different implementation than it has in FFXIV, where it's a giant walking time machine; they're different to the point where I think it would be more confusing instead of less to try to evoke and reference both simultaneously. You start letting in other games, we have an even bigger nightmare: neither of them have anything in common with FFXI's implementation which went for 'ancient mecha', or Type-0's, where it's essentially the in-universe equivalent of the atomic bomb. (All of that's why I'm genuinely extremely interested in seeing how the FF MtG set handles Alexander, but that's beside the point!)