There is no typical relationship with a shortline yard and an interchange. Since most shortlines inherited track, I think most have whatever yard they have somewhere other than where they interchange. Think about the Strasburg RR in Pennsylvania. They interchange with the PRR on the northeast corridor, and their main runs to Strasburg where they have an engine house and yard.
I think from a full-size geography view (room-size) you gain the most penninsula putting it parallel to the long dimension in the room. You could even try a plan where the peninsula is diagonal across the room.
I like the new track work for the interchange. Avoiding S-curves is always a good idea when possible.
