Can you use binary files to reverse engineer cpu architecture?
This was certainly possible with early microcomputers such as the Altair 8800. Each instruction or data value was encoded as a binary number, set up by flipping a line of toggle switches up or down, and when the switches were all set correctly another switch was used to write that number into the next memory address.
Once you have done this once or twice you realise how tedious it is. Hence the rapid development of peripherals such as paper tape readers, punched card readers and eventually keyboards, all of which require some sort of operating system, even if a primitive one. In parallel, programming aids such as assemblers, programming languages, compilers and IDEs made programming simpler and quicker, at the cost of creating distance between the programmer and the hardware.
I doubt it would be possible to write binary instructions directly into the memory of a modern laptop, partly because of all the layers of peripherals and operating system functions that stand between you and the CPU, and partly because such a feature could be maliciously misused, so there are security features that prevent it. But it is certainly possible with a microcontroller board such as an Arduino - or you could build your own Altair 8800 !