What exactly does it mean or imply?
It implies that Kagrenac might throw away Dwemer souls just for experimenting, but that this was a different situation. The "so many" does not mean as opposed to all of them, it means as opposed to only a few. "So many" can still include "all."
Hmm alright, I read this as well. While widely accepted, it's not exactly the truth though? I mean it's a fan made response.. and Bethesda could do whatever they want with the Dwemer lore I'd assume?
It's been explicitly stated by ex-dev MK that the Dwemer became the skin of Numidium. And yes, Bethesda can do whatever they want with the lore, but that's a moot point. They could decide all Daedric Princes are actually bunnies in costumes and that Nirn is actually New York City. We are left to make conclusions based on what we know and assume that's the lore that will be upheld in the future, not based on the endless possibilities of what could happen just because Bethesda can do whatever they want. It's the only theory that makes any sense and has actual lore to back it up.
This theory is further backed up by the events of Skyrim, where we see Arniel Gane disappear when using Keening on the Warped Soul Gem. He becomes bound to the nearest potentially divine being; in this case, the player-character.