The dwemer hate daedra and aspire to be aedra. This is a belief close to all elves, but the dwemer seem to be the only ones that have ever gotten close or even achieved the goal of becoming aedra. I personally think that during the siege of Red Mountain, when the Dunmer invaded from the surface and the crazed Falmer from below, Kagnerac used Keening, Sunder, and Wraithguard to send his race to Aetherius, TES' "heaven".
The dwemer condescension towards the other races of the world very much isolated them from men and mer alike. It caused them to war with many others, but generally the dwemer's technology allowed them to prevail.
The dwemer mined a light blue colored mineral called aetherium in Skyrim until it was depleted. Its color matches both the geode veins and bioluminescent mushrooms found in Blackreach. This leads me to believe that the geode veins are related to aetherium, which makes aetherium a type of soul gem. This would more directly link aetherium to Aetherius, besides the name similarities. So my theory is that Kagnerac used the power from the Heart of Lorkhan and a lot of aetherium as a conduit to send his race to Aetherius. A similar effect was observed when Arneil Gane of the College of Winterhold struck a warped soul gem with Keening and disappeared.
Visual comparison:
Aetherium
Geode Veins
Mushrooms