All the dependencies on bitcoin-config.h.in are in src/Makefile, while the build rule for it is in ./Makefile. Since ./Makefile has no interest in bitcoin-config.h.in, it never rebuilds it; and since src/Makefile doesn't know how, it assumes it is a static file. Thus, it is only ever rebuilt when autogen is run manually.
I don't know a good way to fix this.