The tower is more than just a battery and a conduit, the sources I posted above state that it's actively taking energy from the sun and then eventually concentrated solar through Dalamud and is referenced as doing such as recently as Shadowbringers. Also stated above, the tower was originally used to power the empire and did so for hundreds of years before Xande's revival and subsequent war against Meracydia. But the amount of sun on the surface of Hydaelyn wasn't enough to power the voidgates that the revived Xande wanted to make so Bahamut was sealed in Dalamud and sent to space as a solar collector to send concentrated solar power down to the tower. The Crystal Tower and any power from the lake are separate things that seem to not have much to do with each other as far as we know right now.
Nothing at all in the game or outside it says anything about the Crystal Tower having anything to do with the great amount of aether in the region while there's plenty of sources saying that it's a power plant that harvested the energy from the sun instead so there's no reason until we have more information to suggest otherwise. An aether-rich region would be the perfect spot for an empire based around a mage army and it also happens to be smack-dab in the middle of Aldenard, which is the home continent of Allag. If it wasn't the capital before the conquering, it certainly was afterwards. The Crystal Tower was specifically created to power the empire and its location makes sense if that's where everything already was, not necessarily because they were harvesting the lake aether.
If it did take from the power in the lake, then the region would have suffered while it was powering the empire and there would be no point in mentioning Bahamut harnessing the sun from space when that alone wasn't enough. If the Crystal Tower had absolutely nothing to do with the sun at all like you're suggesting, an easier explanation would have been to say that Dalamud was a prison and the Crystal Tower used him directly as a power souce much like how that battleship in Azys Lla used the Warring Triad. Dalamud concentrating the sun from space and sending it down to the Crystal Tower just augments the tower's existing power generation methods.
Xande's Tomb was originally 1.0 lore but was also mentioned in EE:
While buried there for its aetherial properties, it seems like the Allagans were either incapable of actively harnessing the power of the region directly Shinra-style or unwilling to since it makes no sense for the same source that mentions "the concentrated levels of pure aetherial energy" to also describe the tower as a solar power plant if only one of those things was true and completely miss the tower harvesting the region's aether. 600 years of researchers have concluded that it's a solar power plant and it doesn't make sense for them to be wrong about that while somehow missing the large amount of ambient aether they already knew about.Upon his death, Emperor Xande was interred in a tomb built within a crystalline cavern located in Mor Dhona - reasoning behind this being that it was thought the concentrated levels of pure aetherial energy might repair the corrupted flesh and restore Xande’s soul to his new body. The actual consequences were quite different.
If Doga, an Allagan prince, and G'raha Tia, a person who tied his very essence to the tower and also absorbed memories of Allag both say that the tower collected power from the sun, then there's no other better source and that backs up everything else we already know. If the Crystal Tower was a terrible thing that sucked up the local aether then Midgardsormr would have done something about it. It was around for 300 years before Xande came back and was being used the whole time. It's just that he repurposed it later for reasons that required even more energy than it could provide. Unless there is as-of-yet-unsaid lore related to Emet-Selch's designs, the Crystal Tower's original purpose has nothing directly to do with the navel of the world, high ambient aether, or other shards including the Void.



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