Saying that one employee is the least worst employee you have when someone calls you for a reference means they are the best employee. It also means you aren't particularly happy with any of them, but that's just adding a flavor to the sentiment that this employee is your best.
Now, if I asked you to recommend a bunch of project management/issue tracking software suites, and you absolutely floored me with praise for one, but said good but forgettable things about JIRA, that would be be damning with praise.
Coming full circle, saying that JIRA is the least-worst option means it's the best option and you just have an ideal in your head that isn't being met.
They're utterly different things, really.