The BIOS (well, actually the EFI nowadays) is stored in a flash memory on the motherboard. Not in the processor.

I have never heard of any problem pertaining to the support of PCI Express.

The best you can get today are the motherboards that LibreBoot (a free BIOS firmware): http://libreboot.org/docs/hcl/index.html#supported_list

Unfortunately, there is no solution for current/future x86 architectures: http://libreboot.org/faq/#intel

ARM may rescue us though.

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