There's no good way. I think the dictionary file should allow comments within the json. The json spec says no, but there's no reason not to violate the spec. Then each entry could have a comment like "#canonical", "#misstroke", "#brief", "#preferred usage" etc
Until then, I think the best solution is still to look things up in the dictionary file, but just be careful about it. Analyze the strokes yourself to see which match plover theory, which are misstrokes, and which are briefs. You can tell the misstrokes because they'll probably be at least as long as the theory form and get some sounds wrong. You can tell the briefs because they'll be short. The hardest to identify will be misstrokes for brief forms. But most briefs have at least some kind of logic to them, i.e. something to make them more memorable in relation to the word, or a particular cluster of keys that other briefs use to represent the same clusters of letters/sounds. So you might be able to identify a "misstroke brief" by looking up similar words and seeing if they use similar briefs. And if something really resists understanding, you can always ask on the mailing list, so the answer will be available to all.
Be well,