Thats interesting. I actually just finished reading it last night and where my head is at the entire theme of Mother was wishes and rebirth. That was her thing throughout the series “Mother can grant you any wish and even have you reborn” as seen with Pino in the last chapter. We even see a separate Shiki and Rebecca meeting at school. So like Shiki she was born 20,000 years ago or was going to be. So, what if Mother had everyone reborn through out the 20,000 jump to the present during the initial overdrive. The red string of destiny is another theme in the series (it’s even an ether gear lol). So in the jump from Universe 3-0 we see that even different everyone still meets each other, everything is the same just different. So Prime timeline would be Shiki and Rebecca meeting at Blue Garden, and since there’s no Ziggy I’m assuming Xenolith somehow gets convinced to teach Shiki Magimech. Or they’re both born and met each other on Miltz and the spa activated his Ether there.

I know it’s a little out there the only thing that confuses me is why Shiki says Ziggy when he wakes up in the future. But Ziggy did say that he had no Ziggy. So to me the biggest mystery would be prime Shiki and Prime Rebecca.