Because gpgme treats strings with commas as a stringlist it failes to properly parse default_pubkey_algo that contain commas.
The problem can be seen when looking at the output of gpgme's test/gpg/t-gpgconf it shows a corrupted value for default_pubkey_also if the current default is used.Checked with t-gpgconf that a group value is still a list and the default_pubkey_algo is ok