Replicating on-premise SQL Server instance with hundreds of databases to an Azure SQL Managed Instance
I shared the case scenario with the Azure SQL Database team at Microsoft via an Exchange Mailing list for Azure SQL Databases contributors/MVPs. The answer provided by one of the managers of the team is the following:  "Yes, transactional replication will be the best way at this point if they want to keep the replication running after the migration to Managed Instances."

Hope this helps.