This is related to Other Features #6 in the Dec 2013 readme notes: Entity type subtypes with an auto counter data type can no longer be absorbed
into the parent table. Similarly, no entity type identified by an autocounter
can be created without its own table.
The default data type for the .id reference mode is Autocounter, so object types A,C,E are forced into their own tables, just as if they had been independent. If you had tried to load the DDL from the previous mapping you would have had a failure due to multiple IDENTITY columns in the same relational table for the D,B,XHasC tables. If you switch the data types to something that can coexist nicely in a table created for another object type then you'll see the tables absorb back in.
PS This type of question is probably a better match for the NORMA/Technical Support forum.