It's a really complex issue clearly, as no one would wish to discourage trans individuals from playing sport.
But as I can see it, if trans individuals are included in mainstream sports competition, girls/women are disadvantaged whichever way the call goes in terms of whether trans individuals are included with their birth gender or the gender they identify with.
If the former, then FTM competitors with a newly gained strength/speed advantage beat F competitors, as in this example in the US.
If the latter, then MtF trans competitors beat F competitors with their residual/inherent speed/strength advantage.
What is the answer? The only one I can think of is that competitors with modified bodies are not able to compete with non-modified competitors (the same way as Oscar Pistorius was not allowed to compete in mainstream men's events as his blades actually could have given him an advantage.) I envisage that there would be resistance to this from some in the trans community as it could be interpreted as excluding trans individuals from sports events. But I can't see how else women's sport doesn't end up massively compromised.