The problem is the default/legacy APIs don't use the new paths... in .Net I had this problem a lot, and serious issues every method I tried to work around it would hard crash VS, let alone the application I was working on... in the end, after days trying the solution was to say f*ck it and just put the directory I was working with closer to the root of the drive in question.
Why they can't fix .Net under the covers to use UNC in windows to avoid the class of problem I don't know, understand or comprehend... and that's just one very common platform for windows. I would say the same for npm/node and libuv for that matter.
I use bash a lot in windows (installed with msysgit), and that's got it's own set of problems. More problematic is the number of node modules that rely on bash scripts for builds, that don't work at all in windows.... which makes it very hard to contribute.