both programs will eventually be fully merged. While they are essentially one program under one administration, Latam is still to figure out how to merge them since JJ uses points as "currency" and LA uses kms. There's no equivalence between both.

That's mainly the biggest difference. LA kms can only be used for redemption within the airline. JJ points are part of a much bigger points scheme under the Multiplus point programme. Points are earned by flying but also by purchases in several vendors, hotel stays and the like... and can be redeemed on all of those