The EJB Embeddable Container is used as a test framework, see the TomEE documentation.
In 2014 I used it instead of Arquillian but not today.
Why talking about this granularity that we would prune something from EJB?
Let's prune=deprecate whole EJB or nothing.
I know that removing the EJB in the future may break many users but my argument is that they still may use the application servers with EE 8.0 (javax) or deprecated EE 9.0 EJB (jakarta).
I remember that the Oracle had the ambition to provide EE container based test framework.
The Embedded Container was quite fast to run the tests but it was only EJB!
Probably, and I would appreciate, we should provide some f/w for the Microservices and appropriate EE profiles.
For instance i wrote my own test JUnit Runner / framework on my GitHub with IoC, DI, JTA, JMS, JPA and combined it with Dropwizard to test JAX-RS servlets.
It was as fast as the usual unit tests. Notice that Spring has it's own Runner but we don't!
Additionally, it enabled us for parallel testing (isolated containers without using ClassLoaders).
The EJB Embeddable Container bought the idea of unit testing the EE apps which was maybe a hack on our side of the users but it showed us a direction with CDI and another APIs too.
So yes, let's deprecate EJB now and remove it later but then provide us with some new Embedded Container for very fast testiing of the backend apps.