Is Squirrly SEO fully compatible with AMP?

Yes, Squirrly SEO integrated with the AMP for WP and the AMP plugins. 

If you enable the option shown below, Squirrly will load the Accelerate Mobile Pages (AMP) support when these plugins are detected on your site.  

To reach this option, go to: Squirrly SEO> SEO Configuration > Connect Tools > AMP

By default this option is set to ON.

For more information, check out this link.