While resetting the Base Pose is a one-time event, creating an actual Base object lets you interactively move and adjust the capsule/bone/muscle without affecting the skin geometry.

While in most cases this is not needed, you can do advanced rigging, or allow for pivot adjustment, resizing rigs without re-skinning, and so on with this technique.

To create a Base for a capsule, bone or muscle

1. Select the capsule, bone or muscle object(s) you want to create a base object for.
2. Select Muscle > Muscle Objects > Create Base for selected Muscle Objects.

   When finished, the object(s) you selected are duplicated and connected to the Muscle deformer so that they act as a base object. Moving the base along with the original object lets you adjust the object without affecting the skin.

3. When you are finished with the base, you can delete the base object.