Is it permissible to skip congregational prayer for an individual who is praying alone and is afflicted with obsessive whispers (waswas) about passing wind during prayer, knowing that he can control himself when praying alone?

What you are experiencing is not without one of two possibilities:

First: That you are certain of the emission of wind. In this case, you must perform ablution, and your prayer is not valid without it, due to the saying of the Prophet, peace and blessings be upon him: "Allah does not accept the prayer of anyone of you if he passes wind until he performs ablution." And feeling shy about leaving the row is not a justification.

Second: That you are not certain of the emission of wind. In this case, you are considered to be in a state of purity, because the original state is purity, and what you feel might be from the whispers of Satan, due to the saying of the Prophet, peace and blessings be upon him: "If one of you has a doubt in his prayer and does not know whether something came out of him or not, he should not leave until he hears a sound or perceives a smell." And one should not give in to whispers.