you've mentioned the old features in your solution that are somehow activated automatically. This is mostly likely possible because of the so called Feature stapler. This feature stapler allows you to automatically activate custom features when a certain site template is created. You can try searching for "FeatureSiteTemplateAssociation" word withing all xml files of your solution.
This xml file might looks like this:
<?xml version="1.0" encoding="utf-8"?>
As you will probably see, this file already contains one or more feature associations. You just need to add yet another one for the feature that needs to be activated. Here is a sample: