Is this something that can be addressed with further enhancement of the Windows implementation of PHP (or IIS), or does this issue run deeper? For example, is this as a result of the way NTFS works?
It's not the result of the way NTFS works. There are a few factors which are contributing to a small overhead per-call on filesystem operations, and unfortunately PHP tends to be very heavy in its use of the filesystem, and so the performance degradation is exacerbated on Windows.
And, yes, it's being looked at... We're looking for ways to optimize this area in order to close the gap on performance.
G