66:12 And Mary, daughter of Imran, who guarded her chastity, and We breathed into her (baby) from Our Energy. And she put faith in the Words of her Lord and His revelations, and was of the most devoted servants. [In very adverse circumstances, Mary guarded her chastity and revolted against the non-Divine institution of monasticism, and got married adopting the natural family life. ‘from Our Energy’ = Free will, as all human beings are granted. 2:30]
Allah breathed into her in the same way He breathed into humanity, see my other posts on breathing in meaning revelation, knowledge, consciousness.
If Allah breathed into Mary and she conceived by Him, then He begat Jesus. Can you understand that the doer of an act is responsible for the deed, so He becomes the 'father', Jesus His son, all of which is clearly and undeniably denied by the Quran so you have to change your understanding to do away with the gross contradictions this brings up.
"It is a Fact, God does not beget rather He creates what He wills" is just changing beget for create when the result is the same: BEGATTING