Templates created through the InDesign plugin have subtle color differences from my InDesign document. How can I prevent this?

The InDesign Plugin will use the InDesign PDF preset named "edocbuilder" to export PDFs. If you need any special settings in your master PDFs when the plugin uploads from InDesign, you should modify this preset. This video shows the process of modifying this preset for some specific color management settings: https://www.screencast.com/t/7dyKbVYw