I might be wrong on this, but I think it's important to remember that Alexander creating time loops was born from the primal's own desire to minimize its "footprint" on the world. As primals consume vast quantities of aether, both due to their existence and the use of their natural power, any time travel Alexander did would have a significant impact on the surrounding environment. I recall this being the reason it decided against using its power to do such things as stopping the 7th Umbral Calamity. Rather than dismissing it as impossible because it hadn't already happened—which would be the case if time travel only allowing causal loops was a universal rule—Alexander chose not to do so because the cost of attempting it would greatly outweigh the benefits of stopping Bahamut.

In other words, I don't think the inconsistency is on Shadowbringers/the Eighth Era for introducing a split timeline, but rather that it highlights an inconsistency in the Heavensward/Alexander era. To wit: If time travel must resolve into a causal loop, why does Alexander believe it can change the past? And if time travel must resolve into a split timeline, why does it seemingly resolve into a causal loop?

I can just assume that Alexander, as a literal machine god, calculated exactly how to make time travel play out the way it needed to. And I think that's what the writer was going for, but I imagine "God did it" isn't the most satisfying solution to the problem. Also, there might be two or three extra timeline splits because of Alexander's interference. Maybe. I would have to go back and play/read through the plot of the Alexander raids to map that out.