Hi sangchul,
As you already wrote, it is clearly stated "The ISE Configuration backup includes system and trusted certificates, and does not include internal Certificate Authority (CA) certificates." System and trusted certificates are the ones that you see under Administration / System / Certificates / Certificate Management:

Internal CA certificates are the ones that you see under Administration / System / Certificates / Certificate Authority:

Having that said, there is a bit overlap in between - certificate used for ISE Messaging Services is most often one issued by ISE, for ISE. This certificate is located under System Certificate, but it's CA Chain is located under Certificate Authority Certificates.
What I usually do is that I always keep offline backup of externaly issued certificates (which I use for Admin or EAP Authentication, and portals), along with their CA certificates. For ISE Messaging Services, I re-generate ISE Root CA and reissue this certificate, when needed. However, I almost never use ISE CA for any other services, so I can afford not to care about this topic. If you are using ISE CA, you need to export and backup those as well, from ISE CLI.
Kind regards,
Milos