Just a thought, AutoMagiCache
automatically strips the
tag (understandably so), perhaps it should be stripping
<link rel="canonical" href="http://domain.com/path.to.custom.twig.template.html">
Not sure it does any good having it on the FC Checkout markup, and ideally would not reveal the location of the custom Twig URL. One could argue to simply remove from the cacheable template, but figured I'd throw out the idea of automatically stripping it from the HTML since I know other things are currently being stripped, too.