The simplest way will be just removing the Default workflow from the existing template's standard value and update/enable it back when needed. Also the new templates needs to be created without any default workflow and setup later when needed.
Note - If you have lot of existing templates, can try execute a power-shell command to set/revoke default workflow.
Anyways you are planning to go with Sitecore first and Unicorn for content sync, so nothing will overwrite your template changes until you revert back.
Anyways no update required here in your case, as you are planning for Sitecore first with Unicorn.