I've found that MikTeX now have both x86 and x86_64 version.
What's the difference between them? Are there are some limitations in the x86_64? Or they are completely interchangeably?
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There are no significant performance differences between the x86/64 versions of MiKTeX. But between MiKTeX and TeX Live, particularly with including, scaling and other operations on pdf pages.
And there is no biber in MiKTeX 64.1
They are the same but you have to know if you system is 32 or 64 bit. This is the difference.