That assumes that what they did actually worked. (partially)
Well the thing is, the Numidium works. It was used by Tiber Septim and others, so that means that the process was sound. They succeeded to a limited degree
if that was their intent. After that, though, they were basically stuck until exactly what I think they did not want happens.
See, the "atheist Dwemer" idea is basically incorrect. Even "naytheist" is pretty inaccurate. "Intended self-theists" is, if I am right, the closest linguistic anolog. They knew there were gods, but they did not trust them to get godding right. So, using the philosophy of "if you want something done right, you have to do it yourself," they tried to become a single race-wide god (it's unclear if this was a widespread hope of if Kagrenac basically divinity-[censored] his entire race). Then they did, broadly, succeed in becoming a god, but now they are stuck under the direct control of non-Dwemer individuals. It's my thought that Kagrenac intended to be the leading intelligence in this new being, but of course that is entirely speculation and cannot be proven.