Is it permissible to perform Istikharah regarding making up prayers and fasts that were intentionally missed, and is choosing not to make them up considered following dispensations or not?

There is no statement from the people of knowledge regarding Istikharah (seeking guidance from Allah) concerning this matter. It is prescribed for you to follow the one among the people of knowledge whose knowledge and piety you trust. There is no sin upon you in following someone who issues a fatwa that there is no need for a make-up (qada'), if he is among those whose knowledge and piety you trust. Indeed, a group of trustworthy and senior scholars hold this view.