The macOS system CA loader took every certificate that has Trust Settings, in the system, admin or user domain, as a trusted root without reading those settings. A root set to "Never Trust" in Keychain Access, or trusted only for S/MIME or code signing, still verified TLS servers.
The loader now evaluates the settings for the SSL policy. A per-user setting overrides the admin domain, which overrides the system domain, and only TrustRoot and TrustAsRoot are loaded. The OpenSSL path shares the helper that the Mbed TLS and wolfSSL paths already use.