Yes, the current system is intentional. If you would like to offer suggestions, I'll gladly take it into account, discuss and offer it to the team."
And for you, they don't scramble AND if you make carbon copies (Wood, Sand, Wind, Fire, Water, Earth, Lightning, Quick) Then you don't EVER need to worry about who goes where. If everyone gets the same Chakra then it works. They apply to whoever is placed in the first position and so forth. So No, there is no "problem" And glad we got out of the way that things are intentional.
To the Mods: Perhaps something that makes it so the best chakra is always used in the first person in the turn order and so forth.
I was thinking of a "page" sort of idea. Once that'll save alot of time and can swap between characters. Edit the names of set pages to "Tank" "Damage" etc.