If you can get the embedded Alfresco to work in a cluster configuration with other instances of the app, then you should be ok.
I.e. App Server Host A Runs application A that talks to embedded Alfresco that acts as a Node A in a cluster with Node B, which is accessed by Application A on App Server Host B.
I don't know of anybody who has done this specifically, though don't see why this wouldn't work. It is definitely not something that is being tested for, but I don't know of any fundamental reasons for why that wouldn't work.