Re: Coding in binary. It makes no difference. Your assembly is binary, just represented in a more human readable form when writing it in assembly.

Re: Manual interaction. Sure there's plenty of old computers where you can flip switches to input instructions or manipulate registers (memory on the cpu). But this is not much different from using assembly instructions except you're doing it live.

You can also create purpose built processors which might be what you mean? Generally this isn't too useful but sometimes it is. FPGAs are an example of doing this type of thing but using software to do the programming of the processor.