In the context of the JIT compiler that acts on the Assembly (containing metadata and intermediate language):
The assembly is generated on the disk by the specific language compilation so as the CLR makes his own independent compilation to convert the MSIL into native code. Is there a visible output created on disk after this compilation? A file/s containing binary code or similar?
Here is a quite explicit article where I found the answer. Basically, there is not an output file and the native code is stored dynamically in memory during the runtime.
When managed code calls a particular method, the compiling function wakes up, looks up the intermediate code (processor-agnostic object code that's similar to the machine code), then compiles the intermediate code into instructions for the available processor. The managed code then saves those instructions in a dynamically allocated location in memory. The compiling function points back to the original method so that the two are linked: When the method in the assembly executes, it executes the processor instructions stored in memory.