I skimmed over the Arabic tafsirs available at altafsir.com and I could not find anyone who has interpreted this part of the verse to mean an intersex person ( خنثى ).
Rather they all explain the verse as follows: To some people Allah gives only female children, and to some He gives only male children, and to some He gives both male and female children (as twins or in separate pregnancies), and to some He gives no children at all.
Many of them have also cited the examples of Prophets to illustrate this. For example Lut عليه السلام had only daughters, Abraham عليه السلام had only sons, Muhammad ﷺ had both sons and daughters, while Jesus عليه السلام and Yahya عليه السلام had no children. Here they ascribe the phrase "He makes them [both] males and females" to the children of Muhammad ﷺ, as he had three to four sons and four daughters.
ويعطي من يشاء من الناس الزوجين الذكر والأنثى ، أي : من هذا وهذا . قال البغوي : كمحمد ، عليه الصلاة والسلام
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فجعل الناس أربعة أقسام ، منهم من يعطيه البنات ، ومنهم من يعطيه البنين ، ومنهم من يعطيه من النوعين ذكورا وإناثا ، ومنهم من يمنعه هذا وهذا
It means, He gives to whomsoever He wills both males and females, sons and daughters. Al-Baghawi said, "Like Muhammad ﷺ" ...
So people are divided into four categories: some are given daughters, some are given sons, some are given both sons and daughters, and some are not given either sons or daughters
— Tafsir Ibn Kathir
Abu Bakr ibn al-Arabi al-Maliki has discussed intersex people in his commentary on this verse, he says that they are included in the meaning of the previous verse يخلق ما يشاء ( He creates what he wills ). However he says that they are not mentioned in the part of the verse which you have asked about, because it only mentions what happens most often and is silent on what is rare:
وأما قوله: {يهب لمن يشاء إناثا ويهب لمن يشاء الذكور} [الشورى: ٤٩] {أو يزوجهم ذكرانا وإناثا ويجعل من يشاء عقيما إنه عليم قدير} [الشورى: ٥٠] فهذا إخبار عن الغالب في الموجودات، وسكت عن ذكر النادر لدخوله تحت عموم الكلام الأول
— Ahkaam al-Qur’an