The above code looks incorrect due to a bug in templates.js
Take a look here
https://github.com/NodeBB/nodebb-theme-lavender/blob/master/templates/header.tpl#L20-L27
You header.tpl should have that block in the <head> tag.
What problem are you having exactly?
If it works for you, keep it up.
The semi-official way to do this is to fork the plugin you want to use, and make the appropriate changes.
Then, add the original repo as an upstream branch (using lavender as an example):
git remote add upstream https://github.com/NodeBB/nodebb-theme-lavender.git
When you want to update to the latest lavender for your theme, merge or rebase:
git checkout master && git fetch upstream && git merge upstream/master
