Is it permissible to fast a day with the intention of making up for a missed fast in Ramadan, and if not, then as a make-up fast, in the event of doubt about breaking the fast due to obsessive thoughts (waswasa) or ignorance of a jurisprudential ruling, such as eating after the time for Fajr begins without hearing the adhan, or intentionally swallowing mucus while fasting?

The cure for obsessive thoughts (waswas) is to ignore them and pay them no mind. There is no need for you to make up for anything you mentioned regarding those situations, nor should you fast as a precaution in the manner you described. This is because doing so is a way of giving in to obsessive thoughts. You should disregard them and not concern yourself with them. The door to voluntary fasting is wide open, but do not open the door of giving in to obsessive thoughts, for it leads to great evil.