I'm really quite unimpressed with Evernote on this issue. So much so I signed up for a forum account to post this. It has now been almost 6 months and 2 days since I first reported this issue after installing a beta of Sierra on my dev test system. A number of workarounds have been presented, but they all involve users jumping through either high risk hoops or switch devices.
Amazingly, Evernote has not resolved this issue. They continue to promote the built-in annotator, but it really is a poor user experience compared to the simplicity of Preview.
I now fear any Mac OS and Evernote updates coming down the pike.