To be really honest, I'm wondering if the design change of aetherytes into Heavensward is simply due to technical reasons - the 'large' heavily detailed ARR style aetheryte works perfectly fine in ARR's smaller zones but would be a bit of a resource hog especially in HW's new huge areas, so the new 'ancient' style aetheryte is smaller and less detailed (notice how the central crystal is much more smoother than the ARR style?) to compensate, to make it less demanding on the system. Camp Cloudtop can get away with it due to the fact much of the Sea of Clouds is... empty space.

So yeah, I think this is just one of those cases of 'form follows function' here and any lore explanation for it is just a handwave to explain the differences in design.