You can replace "have been" with are in these sorts of cases. So "Phrases in green are marked to show passive voice." Or even shorter "Phrases in green use passive voice".
You've perfectly demonstrated the problem with these kinds of revisions. "Phrases in green use passive voice" removes the passive voice, and in doing so, completely alters the semantic content of the sentence. The passive voice expressed a meaningfully different notion.
> Phrases in green are marked to show passive voice.
That's still flagged as passive voice by this abomination of an editor.
> Phrases in green use passive voice.
The meaning of that is less clear than the original. The phrase isn't using anything. We are talking about how it was written: facts about its construction that happened to it. The only way we can do that honestly and concisely is with passive voice because the phrase is only passively involved.