Do changes made to a puppet in a scene apply to the puppet permanently or just to that local scene?

Well, there are different contexts.

• If you change a puppet (eg in rigging panel), that is made to the puppet in that project.
• if you want to use those changes in another project, you have to export the puppet and import into the other project. Nothing is shared between the projects (exporting and import a makes a copy of the files)
• The exception is you can share artwork and change it, it will update in all projects (manually set the path to a common Photoshop etc file)

Next, there are properties for the behaviors. There are 3 contexts here. There is the default values used by the puppet. There is the default value in a scene. And there is the value recorded in a take during animation.

• The first context (puppet defaults) can be changed when in rigging mode
• The second context (default scene value) you can change with the red dot is not on for the property in the timeline panel for the scene. You can revert to the puppet default by clicking the "x" next to the value.
• The third context (recorded values) is when you arm and record a take - the values in the recording override the defaults for the scene/puppet