Currently, clickhouse_connect will silently drop sending settings that already match the server's default. Most of the time this is a sensible thing to do. However, there are some settings such as do_not_merge_across_partitions_select_final that according to the docs

If not explicitly set, ClickHouse will automatically enable this optimization when the partition key expression is deterministic and all columns used in the partition key expression are included in the primary key.

Default value: false (but may be automatically enabled based on table structure if not set explicitly)

can be dynamically changed by the server if not explicitly set. Therefore, it's currently impossible to explicitly set the value to 0, the server's default, to prevent the server from changing it.