There is no way to customize this default template from RStudio's user interface; however, for OS X (similar in Windows) the file is located under:
/Applications/RStudio.app/Contents/Resources/resources/templates/query.sql
So you could potentially modify that file to fit your needs. Notice that I wouldn't encourage to tweak RStudio internal files, but if you really want to or need to, that's one way. I would also encourage you to open a GitHub issue for us to consider adding a proper file-template editing tool within the UI.