Half an hour later, after answering the questions that my Companions had about the pseudo-merging of my Domains, I cleaned up the mess that I made on the surroundings due to the unstableness of the three-Domain merge.
And from that experience, I figured out why it immediately became haywire as soon as I merged the Aether Zone.
It's simple. It's not part of my Transcendent Pathway. Only Psyche and System were involved during this rank.
Although theoretically, it's possible to accomplish it, it requires an impossible level of Energy Control. In my estimate, my current Energy Control was already on par with a Rank 2 Sage but that's still not enough.
Maybe, I could reduce the instability of it once I reach the 4th Realm where I wouldn't need to force the merge of the Domains anymore. But that's still up for debate.