I'm facing the exact same issue. From my digging, it doesn't seem possible:
- PriorityDLTXExtensionManager.findScriptNature always returns the 1st script nature, regardless of the context
- Model.getScriptProject takes a 'physical' project as parameter, and cannot return 2 ScriptProjects
It would be useful if a DLTK expert could confirm, or provide a workaround.