Can someone explain to me why it is so difficult to produce hardware that is identical to current offerings but with software that is different? Is it driver conflicts and BIOS problems?
Because there are lots and lots of chipsets that work somewhere in the range of horribly to not-at-all in Linux (Realtek and Broadcom spring to mind for poor Linux support with their WiFi chipsets). And any driver that hasn't been upstreamed creates a boatload of work for the support engineers, since kernel updates tend to break out-of-tree drivers on a semi-regular basis.
Manufacturers are obsessed with the word "proprietary".
For that reason alone, they tend to keep their drivers closed-source, which means that manufacturer must keep that driver up to date without any help from the outside world.
This works with Windows until a new version of Windows is released that breaks functionality. This does not work with Linux, which is monolithic, and requires drivers to be built into the kernel.