Recently found that lists with custom content types, customized in InfoPath form missing in InfoPath Report. In further analysis it revealed that once I customized the Item content type in the InfoPath form, the lists started appearing in the report. It appears that the SharePoint Assessment and SharePoint Modernization scanner tool only considers if .xsn file is present in the Item Content Type and does not check for other content types in the list. Refer below document for screenshots.
List with custom content type.docx
The above issue is only for the Template type Custom Lists. Incase if a Farm library has custom content type, they are listed in the report. It would be better to scan other content types in lists as well.