3D viewer: persist source transparency on refresh

When refreshing the 3D viewer, transparency set in the selection widget
color wheel was lost and all source coloring was opaque until
transparency was set again in the selection widget. This was caused by
only the ID, base name, and color of the SkeletonModel being persisted
to refreshed space's models. Instead, fully clone the SkeletonModel, and
copy the model's transparency value to the 3D viewer's internal skeleton
representation when constructing from a SkeletonModel.

Also make all coloring modes besides 'source' opaque.

Closes acardona/CATMAID#773.