The big problem is that there's no way for IT and end-users to find out what they're missing. It is possible to dump the myriad registers affecting performance, but they're meaningless to mortals and many can't be changed without disrupting operation. Short of writing your own BIOS, there isn't much you can do. Maybe that will change. The secretive relationship between chipmakers and OEMs doesn't always serve customers well. The configuration advice that AMD issues to its OEMs, BIOS vendors, and OS vendors could form a sort of fingerprint. Even without an understanding of the meaning of individual registers and flags, patterns of variance can point to a vendor's agenda for diverging from best practices. If nothing else, IT could ask why AMD's advice wasn't followed. There may be perfectly good reasons, reasons that differentiate one server brand from another and show who's been doing their homework.
No chipmaker would ever single out an OEM for praise or scorn. AMD's no exception. While AMD's testing engineers express frustration that their recommendations are a take-it-or-leave-it affair, and that when their advice is set aside it affects the public's perception of their CPUs, they don't take it out on OEMs either on or off the record. AMD figures that this is the way the system works when you're on the 20 side of a market that's split 80/20.
The system needs to change. AMD is building new classes of high-powered client platforms that are wide open to end-user parametric tweaking. Enthusiasts and gamers do pay attention to AMD's advice with regard to performance, and they're driven to pull the maximum possible performance out of AMD's silicon. This serves AMD well, because when third parties do this and write about it, AMD doesn't have to out OEMs for taking a lazy approach to configuration. Enthusiast-tweaked machines create a best case, and makers of desktops sold into the high end will have to explain why they don't live up to best case numbers. That's not being done for servers, in large part because server enthusiasts willing to do exploratory tweaking of their machines are rare. I only know one such person.
As mainstream server CPUs grow from four to six to eight cores, four socket servers become the norm and deeply multithreaded applications come to predominate, tuning the CPU, chipset, bus, and memory becomes crucial, with a direct impact measured in dollars, hours, and watts. This is tuning that administrators shouldn't be required to do by hand. They should be able to trust that when a system hits their floor, it performs as well as its technology permits. This requires that vendors put some effort behind understanding and leveraging the differences between AMD and Intel architectures -- effort that isn't a priority at present. This mystifies me, since AMD does all of the legwork, freely handing vendors BIOS and kernel guidance that started taking shape when the CPU was still in simulation. It takes a lot of work to ignore the chipmaker's advice, and so far, I've seen no evidence that it does customers any good.