I don't think they are planning as far ahead as you think they are.

One of the necessary skills of planning serial fiction (and an MMO like FFXIV is serial fiction) is to purposely leave hanging minor plots in a major plot that can then be gone back to and fleshed out. Do it right and it feels like the writers have been planning things out much further in advance then you think they are.

Of course,this can also go the opposite way if it feels too convenient. For me, the writers tied up the story of the 1st Shard and the WoD well enough all the way back in 3.4. I didn't (and still don't) think they need to revisit it. For me, this entire plot seems like an excuse so that the writers can give us a break between an expansion heavily focused on the Garleans (Stormblood) and another expansion heavily focused on the Garleans (6.0). So they decided the end of a finished plot (the 1st Shard and the WoD) wasn't actually the end of that plot and are sending the WoL on a massive cosmology lecture disguised as a side-plot for an expansion.

Now... I hope ShB does have something to do with the plot that started back in 1.0 besides just the greater cosmology, but I don't have my hopes up. If SB's MSQ taught me anything it's that the story team has a major weakness of not making different plots organically mesh with each other and not pacing the MSQ well.