Deploying and running SSIS packages to SQL Server with protection level EncryptSensitiveWithPassword
You can try following:


With EncryptSensitiveWithUserKey - Deploy the project with the same ID through which the agent job will run (I always use SSIS Proxy account created). Also, change the Job owner to same ID or SysAdmin.
You can try to execute the package through T-SQL code (there are stored procedures for this).
Try the command line option in agent to execute the dtexec to run the package.