So correct me if I'm wrong because I think I might be missing something basic here... From what I understand, Alexandrian technology is able to separate separate the soul into 2 different factors - the soul's memory and the soul's life force (life aether). Those are the two parts that comprises the incorporeal aether of the soul. The Endless are not given a full soul and overwriting the memories of that soul. They're given the soul's energy reserves because the Endless itself is just the soul's memory portion (stored in electrope) only without any life aether to sustain it. Together, they form a working function of an "aetheric soul" to be considered alive.
From my Point of View, it's like the hardware (memories that construct a person) and the batteries (life aether) are separated. The hardware isn't being replaced, the battery is. The Aetherial Sea does something similar as it resets the hardware (clean memory wipe after a period of time for reincarnation) but doesn't remove the existing battery. However, Alexandrian technology effectively does the same thing as the Aetherial Sea, just with the caveat of retaining the memories of said people 'who comes back to life' as an Endless with specific racial circumstances (lacking a flesh body because it runs on 'light' as its medium for its corporeal form) instead of being a full fresh start with randomized racial circumstances.
Based on what we know about aether, all the scions during Shadowbringers used a soul vessel during the time their souls were moved out of their bodies. It was comprised of both the auracite for the soul (soul's aether) and the blood infused crystal to carry the memories. They have a lot of similarities in their circumstances with the Endless during that period of time (namely separated components put together creates a working soul again). As noted, the Endless are comprised of memories and life aether to be 'alive', but it's difficult to sustain them.
Which brings about the idea of Allagan cloning. Doga and Unei are effectively dead people who are cloned from the memories of the original Doga and Unei. The clones lived in Sharlayan for a period of time as to find the inheritor of the Crystal Tower. They are effectively manmade, have a direct purpose / program upon their creation and work to execute it. Not unlike the AI of the Endless or even of the Sphene we know. However, Doga and Unei's memories and experiences they made after roaming in Sharlayan and Eorzea are their own. Are they alive then, or can you consider them advanced AI? Their soul is definitely not the soul of the original, but a copy. The originals may be dead, but during the time we met the clones, I consider both Doga and Unei, the two that did their utmost to carry on with the Crystal Tower legacy and creating a path for us to return back from the World of Darkness, I consider them alive as sentient people.
The only reason why the Endless is considered unethical to exist is because the original soul's hardware and battery can't be recycled into the aetherial sea together to create new life when they lose that battery (thus interrupting reincarnation for said soul). If they were to be able to replace the battery source with a sustainable one, then there would be no difference from being 'alive' other than having a different racial features from what your original race was.
To me, the Endless are certainly alive, but the Endless are also clones of the original who lead another life. You can argue whether it is ethical to keep them alive since they aren't the same people as the dead and can be morally wrong for another to take their place, but the residents in Ultima Thule are all technically clones and without a soul too. It doesn't mean they aren't alive either. If you look at them like separate individuals (considering the circumstances of their existence boils down to a full memory wipe after their time is up and a new one eventually takes their place), I don't think it's accurate to say they are not alive.
Hmm... now I think about it... if Allagan cloning technology can replicate life aether that's another plot hole that could've had an easy solution to the lack of life aether problem since G'raha had full access to this technology.