I checked the above mentioned plugin and it seems that it heavily relies on Cordova hooks. For example, you can check the following lines of its plugin.xml
Unfortunately, such hooks are supported only in the Cordova Command Line Interface and thus, the configuration they execute is ignored in AppBuilder. This said, I believe the plugin won't function as expected in other than pure Cordova CLI projects, which is most likely the issue you are experiencing in your AppBuilder project.
Further, I am not aware of any other plugin or approach that allows the usage of iOS9 Universal links in hybrid applications. However, you can still check the Custom URL Scheme plugin
that provides similar functionality. I hope it helps.