Hi @sns ,
After a migration task has completed, you can save it to be rerun at a later date, allowing you to copy only those new or updated files in the source location.
Please refer to this article for more information:
Incremental migration
Whether to use templates in Team sites depends on your actual business needs, it is not necessary. In addition, does custom templates refer to list templates? AFAIK, it is not supported to use site template in SharePoint Online (modern sites) or SharePoint Server 2019 (modern sites).
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