Starting with the 5.0.0.1 release of the plugin and dependent on having a 5.0.0.1+ release of FlexDeploy, MFT Credentials can be created with the MFT plugin. To do so, follow these steps:

Create an MFT project, build workflow, and deploy workflow.
Setup topology. Make sure to add the deploy workflow to the MFT instance(s)
Open the project files of the project and give a name to the credential.
Fill in the Password Property. This should be all capitals. It is a reference to a FlexDeploy Property that will hold the password.
Fill in the Credential Alias. This is the text that you will put in the config plan to reference the password.
Click ok.
Go to the deploy workflow and create a new Environment-Instance Property with the same name as the Password Property that you created.
Go to Topology and fill in the password value.
Make sure that you are referencing the Credential Alias in your config plan.
Build and Deploy your credential and MFT transfer, source, target, whatever is needed.
For future password changes, only the MFT Credential needs to be deployed.
The system is setup so that you will never have to force deploy MFT Credentials.