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I don’t have an answer how to share rigging. I also worry that would you mess up all the recorded tracks if you reimport the puppet again? But that does not seem to be your question.
If you export a puppet file, you are correct that when you import it into the other project it will put it in the gathered media directory. However, you can change the artwork file location after you import it. If you look over in the puppet properties tab at the top (see in blue below) it has the path name of the media file. Click on it to browse to the shared file (and perhaps delete the file from the gathered directory to not get confused). Then at least you can share the artwork file. Does that help?
If I'm reading your post correctly, I have the same issue, but I have done it differently. I'm a song writer, and I animate my children's songs. So there are choruses that need to have the same characters or same animation. I have ended up "splitting" the characters. That way I can erase the behaviors I don't need whenever they come in. And I simply pull the file over. In this screen shot, you can see a series of puppets that are named the same (unfortunately) but look at the colored bars. If I didn't do that, I have to use opacity multiple times to remove them, and keep all the behaviors throughout the song. Look at Sarah1 and see that she comes in 4 times. I generally line them up starting from the bottom.
@SharonfromMD Thanks for sharing your set-up! Always helpful to see how people are organizing their projects in different ways. Really appreciate it.