And I want to comment out the entire selection, then I can't use the Comment Selection command (Command-/) because that simply removes the existing comments. (I think this is a bug in the Source bundle.)

Not a bug per say. It looks at the first row of the selection to decide whether it should comment or uncomment. How do you expect it to know what to do if half the lines are commented and the other half are uncommented? 

However, if I later want to remove the commenting I've added, Change to Column Selection does not work. It seems I am only able to add, not delete, text during column selection. Is this a bug?