1st: Duel Disks just cannot develop their own mechanics, the Pendulum mechanic had to be built into them earlier.
2nd: Edo already said something like Yusho used Pendulums against him.
Either there won't be any explanation about how Pendulum was created, or it'll be that Yusho developed it and build it into Reijis system, but didn't tell Reiji that he finished it before he traveled into the Xyz Dimension. This would also explain how the system knew it was called "Pendulum" from the beginning.
That's just my theorie about it.
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