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Few quick questions,

Has anyone seen a machine that has both an hpet and a real 8259? or is it a case of it always being an hpet with 8259 emulation?
Also, I presume that an AMD based board/cpu would still provide the std. hpet even though its an intel std component? (or they have their own identical equivalent?)

Well AMD pretty much strives to be an Intel clone (even though there might be a few differences in their components sometimes). HPET always starts in compatibility mode. As far as chipsets go - yes, they are compatible. Ever heard about standards such as PC 2001? That used to dictate what a PC must contain.

Thanks for the info, as I thought I still haven't determined if there are any machines that have both, so once you disable compatability mode on the hpet you could still use the 8259 as per normal?

Not that there would be a lot of use for it, more a point of curiosity.

I don't think so. In the past this could've been somewhat more feasible (although I don't think it's been done) as you had separate chips that handled PIT (8254), DMA (8237), etc. Then they started throwing things together; for instance the AIP (82091) handled the functions of the FDC (previously 82078), 2 UARTs (16550), 1 parallel port and the IDE interface; the ISP (82357) handled functions of 2 DMA controllers (82C37), one PIT (8254) and 2 IOAPICs (82093). Nowadays they're all part of the ICH (or southbridge). It's unlikely to have these functions in the ICH and also have another PIT connected via LPC bus. Another issue with having several PIT/HPETs is that they have fixed I/O ports.