I originally implemented Jinja2 on App Engine using the examples shown on the App Engine site here: https://developers.google.com/appengine/docs/python/gettingstartedpython27/te
I guess they are pretty much the same. What webapp2_extras.jinja2 does in addition is that it caches jinja2.Environment() initialization (for the request duration). Plus, you can leverage config/registry system of the webapp2.
Looking at get_jinja2() source you'll see that it's just a handy wrapper for jinja2.Environment() with some default environment args and enabled extensions (e.g. i18n).