In Salesforce, you can grant read access to custom metadata types and custom settings via profiles and/or permission sets. You can read Salesforce's instructions on how to do this for metadata types here and for custom settings here.

For example, for a profile:

And it's the same principle for a permission set; for example:

To retrieve custom metadata types access or custom setting definitions access for a profile, you need to include Profile and Custom object in your metadata filter before the comparison.

To retrieve custom metadata types access or custom setting definitions access for a permission set, you need to include Permission set in your metadata filter before the comparison.

You could use the Default comparison for either, as it includes all these metadata types.

You will find both the custom metadata type access and the custom setting access in the Gearset comparison as part of the profile or permission set itself, rather than being separate line items.

They will be listed as <customMetadataTypeAccesses> and <customSettingAccesses> in the XML in the diff viewer in the bottom half of the screen.

In our profile example:

In our permission set example:

Note that the profile or permission set may appear twice in your Gearset comparison results, so make sure you find/select the one that has this access included. For instance: