His statement, “even if there is an impediment to intercourse”: the pronoun refers to intercourse; that is, even if there is an impediment to intercourse.
His statement, “affecting both of them”: that is, the impediment affects them both. An example is where the man is majbūb (one whose penis has been removed) and she is ratqāʾ (one whose vaginal opening is obstructed). In this case, the impediment is present in both of them: the majbūb has no penis with which to have intercourse, and the ratqāʾ cannot be penetrated.
His statement, “or one of them”: that is, the impediment affects one of them, such as when he is majbūb while she is sound, or she is ratqāʾ while he is sound.
His statement, “whether physical or legal”: that is, even if either of them has a physical or legal impediment. A physical impediment is as in the examples mentioned. As for a legal impediment, it is like one of them fasting, or both of them fasting an obligatory fast, for one observing an obligatory fast is not permitted to have intercourse. Likewise, if he is brought in to her while he is in the state of iḥrām, or she is in the state of iḥrām, the waiting period is established even where there is a legal impediment.
Thus, valid seclusion requires that the woman be consenting, that he know she is present, and that he be physically able to have intercourse.
His statement, “or who has had intercourse with her,” is coordinated with his statement, “who has been alone with her.” That is, if a woman has been sexually penetrated by her husband, the waiting period is obligatory, even without seclusion. How can he have intercourse with her without seclusion? This may be imagined if, for example, a discerning ten-year-old is in the room with them and he has intercourse with her; in that case, he has not been alone with her.
His statement, “or dies leaving her behind,” is likewise coordinated with “who has been alone with her.” That is, the waiting period is obligatory for a woman whose husband dies, even without seclusion and even without intercourse. Death makes the waiting period obligatory without qualification.