Most compilers have a front end, some middle code/structure of some sort, and the backend. When you take your C program and use clang and compile such that you end up with a non-JIT x86 program that you can just run, you have still gone from frontend to middle to backend. Same goes for gcc, gcc goes from frontend to a middle thing and a backend. Gccs middle thing is not wide open and usable as is like LLVM's.
Now one thing that is fun/interesting about llvm, that you cannot do with others, or at least gcc, is that you can take all of your source code modules, compile them to llvms bytecode, merge them into one big bytecode file, then optimize the whole thing, instead of per file or per function optimization you get with other compilers, with llvm you can get any level of partial to compilete program optimization you like. then you can take that bytecode and use llc to export it to the targets assembler. I normally do embedded so I have my own startup code that I wrap around that but in theory you should be able to take that assembler file and with gcc compile and link it and run it. gcc myfile.s -o myfile. I imagine there is a way to get the llvm tools to do this and not have to use binutils or gcc, but I have not taken the time.
I like llvm because it is always a cross compiler, unlike gcc you dont have to compile a new one for each target and deal with nuances for each target. I dont know that I have any use for the JIT thing is what I am saying I use it as a cross compiler and as a native compiler.
So your first case is the front, middle, end and the process is hidden from you you start with source and get a binary, done. The second case is if I understand right the front and the middle and stop with some file that represents the middle. Then the middle to end (the specific target processor) can happen just in time at runtime. The difference there is the backend, the real time execution of the middle language of case two, is likely different than the backend of case one.