Most compilers use not one internal IR, but rather a successive series of IRs. LLVM itself has its normal IR layer, plus a machine IR layer for actually generating code for targets. Plus another layer (two actually, you can pick which one you want) for going between LLVM IR to machine IR. Most programming language frontends have their own IR (or two) that they use in between the AST and something like LLVM IR.

The genius of LLVM is that it's a stable, well-defined IR layer in the middle of the compilation stack that lets you switch out either the frontend or the backend without having to do the entire messy, boring, critical implementation of the other piece. And you can support pretty wacky frontend languages or pretty wacky backends (people compile LLVM to C source or FPGAs, for example).