A question on physical locations of the registers in ATmega328P
You are confusing CPU registers and SFRs, Special Function Registers.

CPU registers only exist within the CPU core. SFRs exist within the RAM bus's memory map. 

CPU registers are used by the CPU to execute instructions and do calculations, etc. SFRs are a part of the logic of the rest of the chip and directly affect the working of the various peripherals.

As far as the CPU is concerned an SFR is just a bit of SRAM, but it affects physical workings when written to, and reflects physical states when read from.