Ya gotta love Margaret.  As great flame-bait column as you would want to liven up those hot summer days.

My two cents:
1) You are not born a blank slate.  Read the Steven Pinker book on this.  There is a lot of left-wing ideology built around people being a blank-slate & hence infinitely malleable like a piece of wet clay.  Biologically, it just ain't so.
2) Identity papers are just that.  On examining them against the physical you, I should be able to say that you are who the document says you are.  As noted, for the over 99% born with one set of biological sexual organs, you are biologically that sex.  Your ID papers should say so.  You don't want a glance at your naked groin or a DNA test to disagree with your ID (but see below).

Perhaps there is an argument for a second piece of information stating gender identity.  For a few percent less than 99%, they will be the same value.  Maybe that would be helpful information, but there are scenarios where that would be very harmful.