If you really want “to understand how computers work on the low level”, then it could be argued that neither Arduino nor Raspberry Pi are suitable. Both of these platforms (their hardware and software) are designed specifically to hide the low-level details in order to make it easy for people who don’t care about those details to accomplish their higher-level goals by creating embedded applications.
Instead, I would recommend picking a CPU family that has a relatively “clean” instruction set architecture, and learning how to program it in assembly language. For example, I did a lot of my early coding on a PDP-11 minicomputer, which has (well, had) a very clean 16-bit architecture. I’m told that the TI MSP430 family is very similar. On modern 8-bit families, it could be argued that AVR is a bit cleaner than PIC. Or you could go old-school and look at the M68K or even the Z80.
So, it really depends on what your goals actually are: Do you want to create embedded applications, or do you want to study the processors themselves?