No. If someone asked you to recommend two employees, and you absolutely gushed about one, but then said the other is "always on time" and "reliable worker", etc. that would be damning with faint praise.

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.

"Damning with faint praise" is a pretty subtle English idiom. In my experience, it's only used to refer to an instance where someone is socially obligated to offer praise, e.g. a doctoral adviser writing a reference for their student, who gives such faint praise that they intend the recipient to infer that, were they allowed to, they would have been explicitly critical. Since the comment author in question was under no such obligation, I don't think the idiom applies.

It doesn't apply because calling JIRA the least-worse simply isn't praise at all, it's a criticism of all JIRA alternatives.