Alhamdulillah
I solved this after a bit more dives, I found that $model->setData($data)I need to use instead $model->loadPost($data); //Mage_Rule_Model_Abstract, which will be $this->_convertFlatToRecursive($data);//Mage_Rule_Model_Abstract, and then check the index of conditions in the data array, after which the data will be in the desired format for saving, and then for loading, to correctly display the saved rules in the block of conditions.
I will write the whole process, perhaps a small module in some blog. Hope this helps someone.
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