In most situations, "scantily clad" does seem to show the speaker's judgement of that person, so I'd say, yes, it is usually negative. To sound more neutral, you could simply describe the person's appearance plainly by saying that they are "wearing little clothing." Some people might say that a person "dresses comfortably" while at home, which sometimes means that they are wearing less than what they would in public or simply wearing pajamas or clothing like it. If a person is in their underwear, you might describe them as "half-naked."
I think how you describe a person's appearance depends on the occasion and the intention of the person for wearing what they are wearing. If clothing is not suitable for a particular event, then you might say that they are "inappropriately dressed." If you want to describe a person's clothing positively despite it being revealing, you could describe it as "fashionable," "beautiful," "seductive" (if you want to draw attention to its revealing nature), etc.