You can use partition software like Partition Master to create a partition and make it hidden. The problem, is, the big PC (and notebook) maker's use a specially modified BIOS to provide the necessary prompt to recover from it. I have made a 40+ year hardware support career avoiding programming so I don't know how hard that would be, but I would think if the user upgrades his/her BIOS, any customization you did would be lost - unless you had a custom made firmware BIOS chip made by Award or Phoenix for each motherboard you use. Sounds expensive to me - especially with just a handful of like motherboards at a time as opposed to the big makers who move 1000s of identical boards per month.
Like you I prefer quality to quantity.
Well, in terms of "quality", the big makers, for the most part, assemble "reliable" parts to make a computer that typically will provide years of good service - with the notable exception of cheap, generic, barely adequate PSUs used by some budget models. I don't allow the use of cheap, generic, barely adequate PSUs in my builds. And I don't allow the use of cheap cases either. A good PSU and case form the foundation for a computer that will provide years of service AND upgrade options - plus, and
most importantly, provide good cooling options.
Some makers allow you to make minor customizations to the computer before purchase. But when I build a computer for a client, I get to know him or her first, and we sit down and I basically do an interview and determine exactly what they will be using the computer for, and [attempt to] determine what their future requirements might be so I can build today a machine that will support future upgrades without having to do a whole new rebuild. In fact, my business model is we build the computer WITH the buyer, not for them. That is, they pick the parts and assemble them, install the OS and setup the machine with us watching over their shoulder. In this way, they learn, and more importantly, they get familiar and comfortable with the hardware. They learn how to handle RAM modules, motherboards, cards, etc. and they learn how to deal with ESD, practicing safe computing/malware prevention and how to keep their systems clean of heat trapping dust - without being afraid to open the side panel.
Yes, that means they cannot walk in my shop and buy a PC off the shelf today. And yes, that means if something goes wrong in the future, they will be more likely to deal with it themselves, but that is actually what I want - for users to be self-sufficient. My business actually stays alive through word-of-mouth advertisement as my clients tell their friends about us.
Personally, I think it is very difficult, if not impossible for a small, independent builder to make a living building PCs. And with the proliferation of smartphones, tablets, and cheap (almost disposable) PCs, it will become harder. Malware removal, upgrades, and repair is where the money is, but even then, the overhead can be expensive - especially if you have a separate shop (mine is in my home). Basically I do it to stay "current" with technologies - not for the money. So my perspective may be different from those who need the money to put food on the table. I make a little on each build, but my main pay is the warm fuzzy I get when my client turns on a PC he or she built, and I see a beaming smile of pride and a sense of accomplishment from them.