One way around it if at least your toplevel VI has a diagram: Specify "Small target file with external file for subVIs" as built option.
After the built, you can substitute your own llb with the diagram-less VIs as data.llb. You might have to make a few dummy VIs with the same name for the built so they are called correctly. Seems to work, but sounds painful.
Maybe there is a better solution somewhere. I'm curious.