Non-embedded extensions are for cases where it is not feasible to embed your application in Mantle's layout due to UI, technical stack, or other restrictions. They will not be able to integrate as seamlessly with Mantle's UI, though they can still make use of the same UI libraries to provide a similar look and feel to embedded extensions.
Another difference between non-embedded extensions and their embedded counterparts is their authentication mechanism. Non-embedded extensions do not have access to the Mantle app bridge and must therefore rely on hmac params verification on the initial incoming request from Mantle.