gpg --gpgconf-list emits several different pieces of information. Some of the information (like default_pubkey_algo or use_keyboxd) will change when set from the command line or a config file. Other data points (like debug_level and compliance) appear to emit static data based on compiled-in defaults, even if the corresponding options are set from the command line or in a config file.
With an entirely empty configuration (no gpg.conf, no common.conf), using gpg 2.4.7, you can see this pattern of inconsistent behavior:
0 dkg@bob:~$ gpg --gpgconf-list debug-level:16:"none: compliance:16:"gnupg: default_pubkey_algo:16:"ed25519/cert,sign+cv25519/encr: compliance_de_vs:16:0: use_keyboxd:16:0: 0 dkg@bob:~$ gpg --default-new-key-algo bananas --gpgconf-list debug-level:16:"none: compliance:16:"gnupg: default_pubkey_algo:16:"bananas: compliance_de_vs:16:0: use_keyboxd:16:0: 0 dkg@bob:~$ gpg --debug-level guru --default-new-key-algo bananas --gpgconf-list debug-level:16:"none: compliance:16:"gnupg: default_pubkey_algo:16:"bananas: compliance_de_vs:16:0: use_keyboxd:16:0: 0 dkg@bob:~$ echo use-keyboxd > $GNUPGHOME/common.conf 0 dkg@bob:~$ gpg --debug-level guru --default-new-key-algo bananas --gpgconf-list debug-level:16:"none: compliance:16:"gnupg: default_pubkey_algo:16:"bananas: compliance_de_vs:16:0: use_keyboxd:16:1: 0 dkg@bob:~$