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There's not rule that says Indra can't transmigrate with a child of a different clan. Just because all previous were Uchiha, doesn't mean that there couldn't be a non-uchiha transmigrate in the future.
and before someone tries to make an argument about them needing sharingan to get rinnegan and all that, please remember this was BZ's influence not Indra's.
As far as we know, indra may have not even known about the tablet. Hago wrote it then BZ rewrote it.
I guess their chakra would still transmigrate through the shinobi lineage. But as I understand it, reincarncation is because there are things left undone from your life. So, they are transmigrating to finish their original goals imo...don't know if that is true or not. So, once they find peace in an acceptable answer to attaining peace for both brothers, then the transmigration should end.