@Steve Ebersole
One of reasons multiLoad method will return entity which associated with the session if exists; even enableSessionCheck == false.
It depends on getRow() method in Loader.class. Check line of 1539 in Loader.class out.

//If the object is already loaded, return the loaded one
object = session.getEntityUsingInterceptor( key );
if ( object != null ) {
	//its already loaded so don't need to hydrate it
	instanceAlreadyLoaded(
		rs,
		i,
		persisters[i],
		key,
		object,
		lockModes[i],
		session
);

Below test case is a result.

SimpleEntity third = session.byId( SimpleEntity.class ).load( 3 );
third.setText("changed entity");

List<SimpleEntity> list = session.byMultipleIds(SimpleEntity.class)
                     .enableSessionCheck(false)
                     .multiLoad( Arrays.asList( 1, 2, 3, 4, 5 ) );
assertEquals("changed entity", list.get(2).getText());

Changed the text in third entity which associated with session.
when executing multiLoad() this changing was not flushed yet, also id:3 would be included in selection of query. ; enableSessionCheck(false);
but results has a changed entity in session.

As a result even enableSessionCheck == false, returned entities are associated with session.
Then including ids which already are associated with Session, don't need to include in selection of query.
I think enableSessionCheck(true); is better than false