I think there are multiple issues.
1) I got all the indexes created, moved it above the "# AUTOGENERATED" and can confirm these indexes in the console. So, even when there are no net new indexes getting added, the file keeps getting updated.
2) Regarding how to set, there is already a "--require_indexes" which if set should be erroring out when a new index is required. So, if this is set, then it shouldn't update the index file, isn't it?