UNIX software is not perfectly portable. Portable software is less likely to run on niche systems. The fewer users that a particular platform has, the less likely it is that portability issues particular to that platform have been discovered and fixed.
It has been my experience that one is more likely to find portability bugs in software when one tries to build it on Interix/SFU/SUA than when one attempts to build on Cygwin.
There are only two reasons to use SUA:
- Interix/SFU/SUA has the advantage that much of its system calls are implemented in a kernel driver, just like native system calls. Cygwin hits a userspace emulation layer for many calls, and that incurs a performance cost.
- Cygwin is third party. Interix/SFU/SUA comes from Microsoft.
- Interix/SFU/SUA includes some fairly useful NIS/NFS integration stuff. It's not great, but it's better than nothing.
Whether you choose SFU or Cygwin, UNIX software ported to a compatibility layer is generally more pleasant than native hosted software. ActivePerl and native Apache are just a pain in the ass compared to Cygwin/SFU's implementations.