Is it permissible to combine the intention for a supererogatory prayer (Salat al-Ratibah) and a votive prayer (Nadr), or between the الاستخارة prayer (Salat al-Istikharah) and supererogatory prayers (Sunan), or must each be performed separately? And if it is not permissible, how can one atone for that?

It is disliked to make a vow. A conditional vow is not binding unless its condition is met. It is not permissible to combine the intention of fulfilling a vow with the intention of performing the regular voluntary (Sunnah Ratibah) prayer, as they are two independent acts of worship. If they are combined in one prayer, then, as a precautionary measure, one should make up the two rak'ahs of the vow prayer and continue making up until it is highly probable that one's obligation has been discharged. As for combining the Istikhara prayer and the regular voluntary prayer in a single supererogatory prayer, it is permissible, though it is better to perform each separately.