I noticed that classes which are not in the default visible modules are excluded from the classlist:

skip writing class org/omg/CosNaming/NamingContextExtPackage/InvalidAddress from source jrt:/java.corba to classlist file
skip writing class org/omg/CosNaming/NamingContextPackage/NotFound from source jrt:/java.corba to classlist file

skip writing class javax/activation/SecuritySupport$1 from source jrt:/java.activation to classlist file
skip writing class javax/activation/MailcapCommandMap from source jrt:/java.activation to classlist file

skip writing class javax/xml/bind/annotation/XmlAnyAttribute from source jrt:/java.xml.bind to classlist file
skip writing class javax/xml/bind/annotation/XmlElementWrapper from source jrt:/java.xml.bind to classlist file

skip writing class sun/security/smartcardio/SunPCSC from source jrt:/java.smartcardio to classlist file
skip writing class sun/security/smartcardio/SunPCSC$1 from source jrt:/java.smartcardio to classlist file
skip writing class sun/security/smartcardio/SunPCSC$ProviderService from source jrt:/java.smartcardio to classlist file
skip writing class com/sun/deploy/security/MozillaJSSProvider from source jrt:/jdk.deploy to classlist file