No, the SD card has FAT32 filesystem. I don't know how you mean that no windows program can read it, it should be. However it also has a partition table so it should be handled that way. About the Xemu binaries, I've already posted where they are in the previous post in this topic:
For example, xemu-binaries-win64.zip for 64 bit windows. That's true anyway, that these binaries and older than versions can be compiled from source _currently_.
Actually the mega65 emulator within Xemu does not even require those rom files at all. It only requires the C65 ROM but it's on the SD card image file.