I think the completely comprehensible system has always been an illusion. There's always some cutoff level below which people don't understand (or don't care to understand) the system they're working in.

The old Apple 2 hackers had a great understanding of assembly, but that's because it was the top level of the system to them, the stuff they worked with daily. I doubt most of them understood the PLA that decoded the instructions, or the behavior of the dynamic NMOS logic inside the 6502.

The 6502 instruction set was essentially the API of the processor, and it wasn't above reproach any more than current software APIs are. Many people wished for different addressing modes or additional instructions to simplify common coding tasks.