This is not theoretical; it happens quite frequently. For toolchains, in particular I'm aware of how Apple (not that they're unique in this) has "blah blah open source" downloads, but often they do not actually correspond with the binaries. And not just "not fully reproducible but close" but "entirely new and incompatible features".
The ARM64 saga is a notable example, which went on for at least six months (at least Sept 2013 to March 2014). XCode 5 shipped with a closed-source compiler only for all that time.