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

When an InDesign document is uploaded using the plugin to create a template, the document is exported to a PDF file that is used as the master PDF file for that template. The master PDF is exported from InDesign uses the export PDF functionality available in InDesign to do that. When the PDF is exported, a preset named "edocbuilder" is used for any settings for the PDF file being created. If you need any particular settings in your master PDF file, you may need to modify this preset.
From the File menu in InDesign, choose Export. A file save window will open, so give the file some name, and Save as Type of Adobe PDF (Print) (*.pdf), save it, and then the Export Adobe PDF window will open. The Export Adobe PDF Preset dropdown menu will have any named presets showing on it. You can choose the edocbuilder preset from the dropdown menu, and modify any settings that need to apply to the master PDF file for the template you are creating.