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x86 refers to an instruction set, originally developed for the 8086/8088 CPUs (the 8088 was used in the original IBM PCs and the 8086 was used in the Compaq Desktop). Every CPU since then, from the 80186 (which was used in a 3Com file server) through the 80286 (the IBM AT), the 80386 (the first 32 bit member of the family), the 80486, the Pentium, Pentium II, Pentium III and Pentium 4, have all shared a core instruction set (with lots of additions and extensions along the way). Even the Itanium supports the x86 instruction set.

During a TiVo upgrade you should never boot into Windows, so the version is irrelevant. The reason to use a FAT based system is so that you can mount the FAT drive under Linux, and write the backup to that drive. NTFS partitions can be mounted for read access under Linux, but mounting them for write access is unreliable.
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