The UniFlash tool is fully supported under Windows for production programming of Sitara processors. What is not necessarily suppoorted is the creation of the "metafiles" that UniFlash tool will use. The reason is that the "metafiles" are actually a full Linux kernel that mounts a network interface (RNDIS if USB) to perform a host to host file transfer.
Cross compiling a Linux kernel under Windows is very difficult, therefore we do not officially support it. This is ussually not a problem, as most serious software devlopers are already using Linux (a Unix clone) as their host development environment for Sitara, even if their Sitara target application not using Linux. Windows in gereral is not a great development environment for advanced software/firmware development, and in fact, most Windows development tools (including CCS) emulate a Unix like environment using Win32 builds of traditional Unix tools.
The metafiles are typically produced by engineering using Linux, and UniFlash can use these under Windows [or Linux] for production line programming.
Thanks,
Stuart