thanks @varshilmehta!
I am actually thinking a situation where you compare statistics for journals using the plugin and for journals not using the plugin. Our site theme has a “top articles of the week” stat in the site front page. At the moment it is counting the downloads, but that is of course not fair for journals with embedded HTML. I will have to find out what COUNTER says about this.
Do you know if there are some meta tags etc. for Google scholar to tell that the full text is on that page? I was looking that it would be maybe possible to add a feature to embedGalley that adds the XML references and list them for google scholar: Improve Google Scholar exposure with reference metatags!