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I looked quickly at _Py_InitializeCore() and I'm not sure that it's designed to replace an existing configuration.
Example:
int Py_HashRandomizationFlag = 0; /* for -R and PYTHONHASHSEED */
(...)
 if (!core_config->use_hash_seed || core_config->hash_seed) {
 /* Random or non-zero hash seed */
 Py_HashRandomizationFlag = 1;
 }
If Py_Initialize() sets Py_HashRandomizationFlag to 1, but Py_Main() doesn't use an hash seed, Py_HashRandomizationFlag value remains 1 which is wrong.
pymain_read_conf() fills _PyCoreConfig from global configuration flags, but then global configuration flags are supposed to be set from the global configuration flags.
So maybe for this specific case, _Py_InitializeCore() should always set Py_HashRandomizationFlag. But it was just one example to show that right now, _Py_InitializeCore() doesn't seem to support to be called twice with two different configurations.