Users would select a variant, and if it supports randomization, the two players would agree on a seed, and enter that on both sides, and then the variant would be randomized according to the given randomization groups. Those randomization groups are just a mask of numbers that states what piece-positions may be swapped. If the mask spans multiple boards, the swapping is to be applied the same on both boards. Swapmasks would be run in-order of their numbering.
This is the replacement issue for the pr #68