Is it permissible to read missed parts of the Qur'an along with the daily allocated parts in the Ramadan ختمة (complete recitation), or is it obligatory to adhere to the order of the Mushaf?

There is no harm in reciting the Quran out of the order of the Mus'haf, though it is better and more preferable to recite according to the order of the surahs. It is permissible to deviate from this order, as many narrations have come to that effect. The prohibition against reciting the Quran "manqoosan" (inverted) refers to reciting from the end of a surah (definition) to its beginning.