I don’t think it’s helpful to bring up intersex conditions as a trans “gotcha!”
In the past, babies with ambiguous genitalia were operated on so that they looked more like vulvas and then raised as female (this actually happened to a child my family knew in the 80s). The scenario you describe with an intersex baby being raised as male most likely wouldn’t have happened, purely due to the absence of a recognisable penis.
I actually don’t know what happens with babies born with DSDs now and I’d be interested to know. Presumably, now genetic testing is available, they have their sex chromosomes checked and are raised accordingly?