It's useful whenever you don't know the value of an integer but would like to allocate space for it now, and then fill in the value later. Many have mentioned length-prefixed data, which is a good example. Another use case is static linking. I believe LLVM uses this when generating WASM object files.
I think this is probably the real reason such encodings are considered valid. The webassembly spec is explicit about allowing valid over-wide encodings:
