Physiological changes like deepening voice, facial structure, muscle mass, and breast tissue.
I'm sensing a bit of limiting options from you. You want surgery to assign the chromosome indicated sex to the child before puberty. How capable are children up to age 11 to make decisions on surgery with their body with respect to their sex? Identify genetic sex and perform the matching surgery.
Looks like you're quoting the rate for ambiguous genitalia. Intersexequality.com estimates that as an inclusive group, intersex occurrence may be as high as two percent.
isna.org, soc.ucsb.edu, a story on Guevedoces from livescience.com, a pdf from interactadvocates.org all do not mention the effects of puberty.
hrw.org mentions "Undescended testes in boys, which is a minor atypicality of the sex organs, requires a simple procedure in early childhood to prevent future infertility."
A story on pbs.org talks about changes during puberty and the use of puberty blocking medication. The effects that are mentioned include changing structure of the face increasing muscle mass, deepening voice, and breast tissue development. Face structure and voice deepening may be the worst parts. Looking at puberty changes in general more inform this more.
The cultural and social issue at hand is how we treat people who do not fit into one of the two narrow types of sexes.