JCMA migrates few workflow rules that belong to Marketplace partner apps on server side as a native workflow rule to Jira Cloud. Here's the list of such workflow rules,

https://confluence.atlassian.com/cloudkb/workflow-rules-migrated-via-jira-cloud-migration-assistant-1031838515.html

We've received a suggestion from a Marketplace partner to provide a way for them to opt out of JCMA natively migrating their workflow rules. For e.g., when a Marketplace partner app provides a mapping for any of the above listed workflow rules via JiraCloudMigrationListenerV1.getSupportedWorkflowRuleMappings() app migration interface, JCMA should migrate them as a Connect app workflow rule to Jira cloud instead of migrating them as a native workflow rule.