The Commentaries didn’t introduce chakras because these are wrong ideas with no reality at all. However, I believe the kalapas and javana cittas are real- a big difference.
I don’t think anyone who has studied Abhidhamma thinks that kalapas or javanas are explained in the Abhidhamma Pitaka - how could they when these terms are not there. That doesn’t mean it is not helpful that the Commentaries explain additional details about nama and rupa. Knowing about kalapas in details helps us to see these elements as they appear now in daily life. And breaks down the idea of a whole.
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