Our long term goal is to serve the scripts at the bottom of the page.

However, if we enable javascripts to be served at the bottom of the page by default (see CONF-12329), plugins with inline scripts may break. For 3.1 we will still serve the scripts in the header with an admin option - Serve scripts in header which will be turned ON by default.

This admin option will then be turned OFF by default for 3.2. If plugins still have inline scripts when 3.2 is released, customers can turn back on this admin config to get the plugin to work again.