Absolutely. Yes, every species is unique. For example, the presence of grazing cattle can help limit grasses that compete with native plants. They can have a positive impact—there's no doubt about that—for certain species under certain circumstances.
Again, listing under SARA requires that we understand the threats and impacts on the land. As for the simple presence of a species at risk on a parcel of land being an indication of habitat health, you'd have to first ask whether that species is declining, stable, or increasing. It goes to the specifics. It can take a long time for a population of long-lived organisms—grizzly bears, even a herd of caribou—to decline and disappear. If they're there but declining, I would argue that doesn't necessarily mean all is good in that habitat.
The specifics do matter, but I agree.