When stashing changes, and with the "Stash staged changes" checkbox unchecked, the staged changes get stashed none the less, and removed from the workspace.

This wouldn't be so bad by itself, except that there is no way to apply only part of a stashed change to the current branch. So when I want to stash changes to only a single file, from a total of 5 files, it becomes painful, especially doing a dance of "commit these, stash that, apply stash, edit stashed changes, edit again", etc.