I agree though it does fall back into the failures of building a believable setting, character writing and lack of meaningful conflict. The issues exist because these three parts are not considered as base storytelling requirements. If you do not write the characters in a meaningful way, ignoring their traits and expertise and flaws you will inevitably fail to acknowledge meaningful conflict and resolution because the setting you have built is in direct conflict with characterization.
I take adhering to lore and world-building disconnect somewhat on an aside because, often times, the way we understand the world is through the characters (and by extension their writer(s) ) and their understanding of the world can change and be expanded upon. You can have something be logically consistent while being tonally inconsistent/subversive (in a negative way).
I would also argue that the process by which the Hanuhanu is not akin to primal summoning as it was stated that it was the use of their magics that stimulated stagnant aether which is actually commented upon shortly after both Koana and Wuk Lamat have competed their trials. The Scions shouldn't make a jump to that kind of conclusion given the context of the situation and would be, if you consider it, in poor taste to compare their crop growing rituals with summoning a deity that has been known (in the context of Eorzea) to be the result and answer to years of oppression and conflict.
If you wanted a better example, I'd look at expectation verses execution regarding the opening of the Golden City gate. The writers had set up Krile with the magical USB stick that has the ability to open the gate. The expectation was that she should use the key to open the gate. This is subverted by denying Krile entry and is resolved by having a npc we met only a couple of hours ago being able to unlock the gate. Does it make sense? Yes, on a technical level because of the permissions set up for royal authority access only. Is it impactful? No, it is tonally discordant as the writes spent the entire game telling us that this was important to Krile only to undermine the emotional core by denying her the ability to resolve one of her CORE motivations/plot points.