Hello,
MBEDTLS_CONFIG_FILE replaces the default configuration file. MBEDTLS_USER_CONFIG_FILE is read in addition to it, so you can use it if you want almost, but not exactly, the default configuration. The advantage of MBEDTLS_USER_CONFIG_FILE over editing the provided mbedtls_config.h is that you can upgrade the library and you won't have to merge your edits with the upstream modifications.
Best regards,