I kinda stumbled on the solution to my problem.  However it's somewhat
of a hack.

I've confirmed that this code works for Create Read and Update:

        public void Override( AutoMap<Configuration> mapping )
        {
            mapping.WithTable( "xCoreConfiguration" );
            mapping.IgnoreProperty( c => c.Application );
            mapping.IgnoreProperty( c => c.Key );
            mapping.UseCompositeId()
                .WithKeyReference( c => c.Application,
"FK_xCoreApplicationId" )
                .WithKeyProperty( c => c.Key );
        }

Previously I stated that I had to have mapping.References(...)
otherwise I would get an error
This code generates fails because it attempted to map the Application
ID twice

        public void Override( AutoMap<Configuration> mapping )
        {
            mapping.WithTable( "xCoreConfiguration" );
            mapping.UseCompositeId()
                .WithKeyReference( c => c.Application,
"FK_xCoreApplicationId" )
                .WithKeyProperty( c => c.Key );
        }

select configurat0_.FK_xCoreApplicationId as FK1_1_,
       configurat0_.Key                   as Key1_,
       configurat0_.Value                 as Value1_,
       configurat0_.CreatedByUser         as CreatedB4_1_,
       configurat0_.CreatedOnDate         as CreatedO5_1_,
       configurat0_.ModifiedByUser        as Modified6_1_,
       configurat0_.ModifiedOnDate        as Modified7_1_,
       configurat0_.Application_id        as Applicat8_1_
  from xCoreConfiguration configurat0_
 where (configurat0_.FK_xCoreApplicationId = ?)
   and (configurat0_.Key = ?)


Adding the mapping.References(...) corrected the mapping of the second
instance of Application ID.  By adding mapping.IgnoreProperty( c =>
c.Application ), the second reference to Application ID is removed
altogether.

Joy.
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