Almost all of the time.
I know of (only) two types of XY DSD where treating the XY person as male could be seen as counterproductive:
Swyer Syndrome, where the genes are XY but development skews female so much that some people have a womb (but not ovaries, just streak gonads that aren't good as ovaries or testes) and some with the condition have given birth after egg donation. When someone's pregnant it's hard to say "the special conditions for women don't apply" - although they won't have suffered from periods or the worry of unwanted pregnancy (or menopause).
CAIS - complete androgen insensitivity syndrome. From the outside look female (albeit maybe taller and less curvy than average) but when puberty fails to come along, eventually the kid gets taken to the doctor and they find out - no womb, no ovaries, short vagina, no pubic or armpit hair.
I don't know of any other DSDs other than the above two where one would have such a real struggle about what the right thing to do is. Maybe other people know though.
I mean, one possibility would be to keep the women's divisions for XX people only and have a special DSD division in the Paralympics. HOWEVER there still seems to be a lot of unwarranted shame about having a DSD, about being different, so I don't know how that would work out. Would the chance to compete for your country help dispell the reluctance to be public about such differences?