I am not entirely sure what your question is but I will try to answer. I think your confusion comes from the fact that some peripherals (typically PCI and APIC) use memory-mapped registers that "steal" memory from the physical address space (the famous 1GB hole described in the blog post). But those memory-mapped registers do not use RAM at all. They simply steal part of the address space and thus some physical addresses that would normally refer to RAM now serve another purpose. Now if you only have 4GB of RAM and the RAM is mapped at 0, a peripheral at 0x10000012C cannot create a hole in the RAM address space because the RAM is mapped from 0 to 0xffffffff. I attached a picture that hopefully makes this clearer.
In summary: when we say "memory-mapped register" what we really mean is "physical-address-space-mapped register", this has nothing to do with RAM.
Note, however, that any peripheral (memory-mapped or not), could also use some RAM, through DMA. But this is a totally different thing because by doing so it does not steal any physical address (and thus does not create a hole).
Finally note that all of this is simplified anyway because there isn't necessarily a unique physical address space in the system, each device may have a different view of the system. See 1 for a relatively clear explanation. Thus in the picture above, I am really referring to the CPU's physical address space.
1: Not your parents’ physical address space, Gerber et al, PDF