OK, after dinking around for awhile, I found that Transpose works if I select two or more lines using Multiple Selection (Ctrl+Shift+L), and then Ctrl+T to transpose characters, words, or lines vertically.
Multiple Selection also enables the commands on the Edit/Permute Selections sub-menu, but Multiple Selection is not required for commands on the Edit/Permute Lines sub-menu.
Edit/Permute Lines/Unique works as expected (removes duplicate lines leaving the first instance), but I can't get Edit/Permute Selections/Unique to do anything. For example, Edit/Permute Lines/Unique changes:
But if I multi-line select the following four lines (selecting the characters), then Edit/Permute Selections/Unique doesn't do anything to:
... although the other commands on the Edit/Permute Selections sub-menu all seem to work as I expect them to. Is there something else I'm missing about Edit/Permute Selections/Unique?