The short answer is yes. I would love to have a 'ship creator' type plugin for Blender. It would, at least initially, be a separate tool from this one, although it could work with it. I have also looked at how to define animations that can be exported as part of the 'include' file that is created, but I have not found a method that would be both useful, and not a lot more work then just defining the animation in code. It is still something I think about.
You can include the location of empties in the include file that is built (optionally). I do this a lot. They define thruster locations, animation locations, light location, etc.
An overriding design goal for this tools is to keep it as simple as possible for people to create and edit mesh files for Orbiter in Blender, which is already hard enough to wrap your head around.
But yes, I've had the same dreams you have.