I implemented the fixes for this issue and HHH-10984 Open together. What I ended up doing is:

1. Add new MultiIdentifierLoadAccess#enableReturnOfDeletedEntities option (default == false)
2. Add new MultiIdentifierLoadAccess#enableOrderedReturn option (default == true)
3. Added Javadoc clarification to MultiIdentifierLoadAccess#multiLoad to see the Javadocs for the above 2 options.

I am not super stoked about the way the ordering happens, at the moment. For now I essentially:

1. Perform X number of batch loads
2. After all the batch loads, come back and build the result List based on the incoming id positions.

I did it this way to also handle de-duplication which is the bug referenced in the first point here.