Basically, this is under the assumption that the Gate in Xenoblade 1&2 is basically Zohar in Gear/Saga, which it's very likely to be true for many reasons. So in Saga, there's this thing called the higher and lower domain, and the lower domain is split into the real number domain (the physical world), and the imaginary number domain (collective consciousness). Anyway, the power of Zohar/Gate is basically to allow those who can access it to shift reality as they wish by using the energy from higher domain, and also allow shifting between domain and dimension.

So, with how the Monado works in XBC and what it's referencing (Monad & Monadology) and without going into too much detail of the Xenosaga stuff. It's highly likely that XBC's pocket dimension is happening inside imaginary number domain. Now, if you also look at some of the references tatsu makes and the fact that Telethia exists on Mira, it's easy to also assume that X happened at a later point in time in the same dimension as XBC. However, that contradicts with the fact that X happened in 2054 and XBC is suppose to have happened tens of thousands of years after that. So my theory is that since Zohar/Gate's power affects both space and time , before the White Whale crashed on Mira, when they were attacked and then get hit by the blinding light, they were actually shifted into the future of another dimension and into the imaginary number domain by the Zohar/Gate. This also help explain the ending and why the B.B. were still functional even though the Lifehold has been lost and why all the aliens race just understand each others when they're all speaking different languages. Because everything is happening inside the imaginary number domain where XBC happened and where human will can directly affect reality and the collective unconsciousness itself. And obviously, the reason why the Aegis was able to do the same thing in XB2, real number domain, is because of the Zohar/Gate. That's why Pyra/Mythra loses her power as the Aegis after the Zohar's disappeared.