Dear Vividua,
Thanks for using the Animate It! Plugin
I am also currently exploring the Layers Framework.
Regarding the classes not working, I am afraid you are right. I have tested the plugin on Layers Framework and the classes put in "Aniamte It Classes" are not being added to the frontend by the framework.
I have found a workaround for this.
For the animation to work, just put the classes in Custom CSS box in Advanced Tab.
Also, you can add div to any "Excerpt" section in order to add animations.
PFA screenshot of how I have animated the back-end:
(Please see the comments for more info)
Live demo of the instance can be found here:
layers.wpdevcloud.com/
Please let me know if you have any queries.
Thanks again for using the Animate It! Plugin.