[In many cases, legacy applications are the sole reason for the continued use of Server 2003.] Those applications may themselves be unsupported at this point, the company that built them may be out of business or the in-house development team may have been disbanded. Any of those scenarios would make it difficult or even impossible to update the applications' code to run on a newer version of Windows Server. Complicating any move is the fact that many of those applications are 32-bit -- and have been kept on Windows Server 2003 for that reason -- and while Windows Server 2012 R2 offers a compatibility mode to run such applications, it's not foolproof.
It's fine if the documentation is highly technical, I've written linux kernel drivers before :)
Hudson's bootkit takes advantage of a vulnerability in how Apple computers deal with peripheral devices connected over Thunderbolt ports during a firmware update. In these cases, the flash is left unlocked, allowing an Option ROM, or peripheral firmware, to run during recovery mode boots. It then has to slip past Apple's RSA signature check. Apple stores its public key in the boot ROM and signs firmware updates with its private key. The Option ROM over Thunderbolt circumvents this process and writes its own RSA key so that future updates can only be signed by the attacker's key. The attack also disables the loading of further Option ROMs, closing that window of opportunity.