If this discussion needs to move then probably vcpkg github or somewhere might be good to start.
From your description it sounds like vcpkg is building the dynamic library variant of protobuf. I’ve usually used the vcpkg.json manifest for selecting which variant to build. I don’t know if vcpkg uses CMake variables when building the vcpkg port itself.
I do know that vcpkg uses a very specific build environment that the vcpkg.exe executable curates when ports are built so that they are always built in an identical environment, meaning it may not be the same as the environment in your CMake invocation.
What I don’t see in your CMakefile is the CMAKE_TOOLCHAIN_FILE pointing to your install of vcpkg.cmake. Is that no longer needed?