So, from my understanding, there are two types of programs, those that are interpreted and those that are compiled. Interpreted programs are executed by an interpreter that is a native application for the platform its on, and compiled programs are themselves native applications (or system software) for the platform they are on.
But my question is this: is anything besides the kernel actually being directly run by the CPU? A Windows Executable is a "Windows Executable", not an x86 or amd64 executable. Does that mean every other process that's not the kernel is literally being interpreted by the kernel in the same way that a browser interprets Javascript? Or is the kernel placing these processes on the "bare metal" that the kernel sits on top of?
IF they're on the "bare metal", how, say does Windows know that a program is a windows program and not a Linux program, since they're both compiled for amd64 processors? If it's because of the "format" of the executable, how is that executable able to run on the "bare metal", since, to me, the fact that it's formatted to run on a particular OS would mean that some interpretation would be required for it to run.
Is this question too complicated for Stack Overflow?
They run on the "bare metal", but they do contain operating system-specific things. An executable file will typically provide some instructions to the kernel (which are, arguably, "interpreted") as to how the program should be loaded into memory, and the file's code will provide ways for it to "hook" in to the running operating system, such as by an operating system's API or via device drivers. Once such a non-interpreted program is loaded into memory, it runs on the bare metal but continues to communicate with the operating system, which is also running on the bare metal.
In the days of single-process operating systems, it was common for executables to essentially "seize" control of the entire computer and communicate with hardware directly. Computers like the Apple ][ and the Commodore 64 work like that. In a modern multitasking operating system like Windows or Linux, applications and the operating system share use of the CPU via a complex multitasking arrangement, and applications access the hardware via a set of abstractions built in to the operating system's API and its device drivers. Take a course in Operating System design if you are interested in learning lots of details.
Bouncing off Junaid's answer, the way that the kernel blocks a program from doing something "funny" is by controlling the allocation and usage of memory. The kernel requires that memory be requested and accessed through it via its API, and thus protects the computer from "unauthorized" access. In the days of single-process operating systems, applications had much more freedom to access memory and other things directly, without involving the operating system. An application running on an old Apple ][ can read to or write to any address in RAM that it wants to on the entire computer.
One of the reasons why a compiled application won't just "run" on another operating system is that these "hooks" are different for different operating systems. For example, an application that knows how to request the allocation of RAM from Windows might not have any idea how to request it from Linux or the Mac OS. As Disk Crasher mentioned, these low level access instructions are inserted by the compiler.
The only thing that runs on "bare metal" is assembly language code, which is abstracted from the programmer by many layers in the OS and compiler. Generally speaking, applications are compiled to an OS and CPU architecture. They will not run on other OS's, at least not without a compatible framework in place (e.g. Mono on Linux).
Back in the day a lot of code used to be written on bare metal using macro assemblers, but that's pretty much unheard of on PCs today. (And there was even a time before macro assemblers.)
I think you are confusing things. A compiled program is in machine readable format. When you run the program, kernel will allocate memory, cpu etc and ensure that the program does not interfere with other programs. If the program requires access to HW resources or disk etc, the kernel will handle it so kernel will always be between hardware and any software you run in user space.
If the program is interpreted, then a relevant interpreter for that language will convert the code to machine readable on the fly and kernel will still provide the same functionality like access to hardware and making sure programs aren't doing anything funny like trying to access other program memory etc.