Blasted and Infernal Tokyo are parallel worlds and you can even return to them later as long as you aren't in the law route, they diverge from Underground Tokyo in the event from 25 years ago where Tokyo was covered by the ceiling. In Blasted Tokyo, there was no ceiling, so it was nuked. In Infernal Tokyo, the angels were defeated and the demons quickly spread around.
In the main timeline, Tokyo was protected by a barrier and put underground due to it, but everything around it was nuked. Mikado was build by God's chosen ones who were taken from Tokyo before that in cocoons (In Infernal Tokyo, the angels that took care of the cocoons were killed and so the people inside the cocoons died too) and 1500 years passed since then, so the crates of the nukes became lakes and you've got modern Mikado. Akira (who became known as "Aquilla" in later years) wasn't among God's chosen people, but he fought through the Sky tower and Naraku and managed to get to Mikado and become its king. This version of Akira seems pretty similar to the one in Blasted Tokyo, having similar plans for the future, but they aren't the same. Blasted Tokyo Akira obviously never had to climb any towers to leave Tokyo behind and go after his sister. In spite of that, what he talks about creating seems very similar to the actual Mikado.
In the main timeline, it seems like Tokyo's timeflow was slowed down. So, although 1500 years passed outside of the dome in Tokyo, it had been only 25 years since then, which is why Aquilla was just a distant historical figure. Jonathan and Walter having different descriptions about the events before the button suggest that they come from parallel worlds. At least, the one that wasn't accompanied by Flynn seems to have come from a parallel world where Flynn took the opposite actions.
Edit:
Regarding the timeflow, it's not made clear if it's Mikado or Tokyo which has a wrong timeflow, but you can see even in the Neutral ending, where Mikado is destroyed, that the surrounding environment around the city seem more similar to Mikado than Tokyo, so I'd say that Tokyo is the anomaly. Either way, there are some npcs that comment on the odd timeflow, like a samurai who you can see in the castle who says that his son seemed older than he should be after he returned from a quest in Tokyo. There doesn't seem to be any definite statement on the nature or origin of the different timeflows though.
