I think there needs to be more nuance in this conversation instead of everything being so black and white. Nikki and other trans activists are up in arms about the notion that anyone would think trans women competing is unfair, they don't even want to have the conversation, calling it transphobic. But the fact of the matter is, sports were separated by sex for a reason, and trans women, while not being men, ARE biologically male.
On the other hand, so many people are such jerks about trans people living, breathing, existing. They go to great lengths to paint all trans women as deviants, mentally ill or "failed male athletes" as another poster put it. Can you all consider that trans women DO exist, and they don't all transition for some nefarious reason? Come on.
Everyone deserves opportunity, respect and dignity. But sometimes we have to navigate making sure people have equity in opportunity without trampling on others.
I think Nikki is right about the following:
Participants in the Boston marathon, like all major marathons are competing for themselves. They are there for the atmosphere, to get the most out of themselves and see where they measure up. When I finish 390/1112 out of all women in a major race, I'm not wondering how many are trans. I'm just looking at my placing and time, feeling a little proud, hoping to maybe improve and moving on. 
But I would have cared more about who I was competing against when I was an NCAA athlete fighting for spots, for my team to make nationals or win conferences. Competing against runners with unfair advantages would have bothered me.
Could it be like what I said before? Increase spots available to women, to account for trans women, while cis women don't lose spots? Could it be to separate the category for trans women and have higher qualifying standards given their advantages? Can we compromise at all on this one?