One can look at the source code to a program, the libraries it uses, the compiler for the language, and the ISA spec for the machine language the compiler generates. You can know that there are no hidden unspecified quantities because programs can't work without being specified.
When you get down to the microcode of the CPU that implements the ISA you might have an issue if it's ill-specified. You might be talking about an ISA like RISC-V, though, specified at a level sufficient to go down to the gates. You might be talking about an ISA like 6502 where the gate-level implementations have been reverse-engineered.
You can take programming all the way down boolean logic if you need to and the tools are readily available. They don't rely on you "just knowing" something.
When you get down to the microcode of the CPU that implements the ISA you might have an issue if it's ill-specified. You might be talking about an ISA like RISC-V, though, specified at a level sufficient to go down to the gates. You might be talking about an ISA like 6502 where the gate-level implementations have been reverse-engineered.
You can take programming all the way down boolean logic if you need to and the tools are readily available. They don't rely on you "just knowing" something.