I was going to add a new setting item - Apps_Game_Center_enabled into the settings page, but some extra unwanted settings were also added to this group. Although, I've already removed these items from the MongoDB. I still saw them in the settings page, it's so weird...

By diving into the codebase, I finally found that we are using PrivateSettingsCachedCollection to cache the settings. With this finding, I solved the issue with the following code:

Inject the following code below

...
const rcSettings = settings.collectionPrivate.find({ group: groupId }, { sort: { section: 1, sorter: 1, i18nLabel: 1 } }).fetch();
const sections = {};
...

// the code to be injected
rcSettings.forEach(({ _id, section }) => {
    const group = 'Apps';
    const whitelist = [
        'Apps_Framework_enabled',
        'Apps_Framework_Development_Mode',
        'Apps_Game_Center_enabled',
    ];

    if (section === group && !whitelist.includes(_id)) {
        settings.collectionPrivate.remove({ _id });
    }
});

Lastly, run meteor shell and .reload to reload the project, you will find the extra settings have be removed from the collection 😆