So you're missing something very important here regarding Meteion. Meteion is a hive mind, she is not a singular entity. So in essence what happened is once she received contact from all her 'sisters' who are all just clones I believe, their collective despair and apathy caused them to speak like a robot due to their collective trauma breaking them. The one who asks for our help is the one who we made contact with in Elpis, and is the one we're ultimately trying to reach during Ultima Thule. This culmination of information and study for someone as magically ultra empathetic as Meteion completely breaks the hive who are shared their reports to each other. So when the hive reports back to the receiver on Elpis, Meteion just goes batshit until she can't hold it in anymore. Which then using Dynamis energy her entire form morphs to the emo goth bird.
Remember, she receives her message just before her breakdown and Hermes immediately presumes it was from the hive collective (which is why he refuses to have her destroyed), so it is easily presumed that Meteion is not being possessed here and that the hivemind has just gone into a existential breakdown from all their findings.
Hiveion/Endsinger is in essence the collective cosmic despair and pessimism of the grander universe all coming to a conclusion that life is ultimately meaningless and we're all going to just die, so who gives a shit? She is the main threat, especially in a symbolic sense as the Scions are far more optimistic about everything. How well she scales on a power level scale? I mean her "song" causes the final days, and she was able to create ultima thule using powerful creation-like magics.
Endsinger's "song" is effectively a siren song that is meant to subconsciously exploit your emotional weaknesses until you just collapse on an aetherical level and take a purely or mostly dynamis form instead. Her whole game was that she can transform aether thin concepts into dynamis concepts through overloading and corrupting their form, which then on death because this is dynamis energy it doesn't return to the aetherial sea. The black Elpis flower and the black smoggy transformation sequence correlate to this idea that the Endsinger's "song" manipulates emotionally vulnerable people and corrupts them like how tempering works. Such as the peddler guy or the son who gets squashed. The flower is meant to foreshadow this idea that depression and despair "dynamis" is colored black, and the rainblow flowers in Ultima Thule are meant to embody all emotions one can feel which is meant to show Meteion that their is so much more to life then hating life.
I'd be very confused if Endsinger wasn't supposed to be the final boss originally as she makes sense on a thematic level (regardless of how much one might think the theme is even good or well executed). You'd have to change pretty much everything to make a different final boss. Also their was the weird morse code with Nero's device that says "ITS ALL WRONG" which while likely not fully intended to mean anything at first, but this same phrase is said by Meteion at some point during her break down which is a call back to that. So I'd imagine this rough theme for EW was intended, and Endsinger captures that theme. Why this morse code even happens I'd imagine it was Nero's machine detecting the "siren song" which just screams hopeless pessimistic drivel enough to drive you mad.
As for how the ancient's power scales...
In fiction, and in actual science through some law of energy that I can't fully recall which one it is, typically the power to create is notably more difficult to achieve then the power to break or destroy. The amount of energy to create things into existence is so much harder to achieve and control then the power to just break it, unless it is complete and utter anhillation on every conceivable level. This is why creation powers on a mass scale are usually reserved for literally Godlike-entities in fiction, while it is a much lower bar to just destroy life and matter on a mass scale.
So the Ancients being able to create life, even if it is not quite as powerful or as intelligent as them, is an extremely high feat of aether manipulation and it is quite easy to manipulate aether to destroy things and if they can channel such things into destruction capable magics (or just do what Elidibus did and just mass create an army to then wreck things) then they are capable of destroying the world. Elidibus is also technically a primal and thus gains aether from prayer and reverence as the "Warrior of Light".
Emet effectively made a complicated glamour and some moderately sentient life like Hermes did with Meteion. Glamours in FFXIV can do way more then just change your clothes. Urianger used one to hide the Waking Sands around HW I think, so glamours can distort the image of large stuctures like it doesn't matter so someone with as much aether as Emet can remake a city as long as he doesn't have to make the city too full of life and complex thought.