The benefit of one of the two automated options is that whenever the model is updated it will automatically update whether or not it suggests IDs for relevant taxa without extra curatorial work. The negative is that it will take a lot of work experimenting with ratios and algorithms and testing them out on different taxa to figure out how to do it in a way that isn’t counterproductive. If we can get any hint from the hybrid reintroduction thread, trying out complex changes to the CV is a slow process.
The benefit of a manual process is that theoretically it should involve less up-front programming work and can be implemented sooner. The negative is that it will require constant upkeep by curators, and there are so many potential problem species that there’s still a good chance of species being missed and accumulating faulty IDs. We don’t have specialist IDers for all taxa, and even where we do not all of them will know about or optimally utilize this flag option. There will also certainly be cases where a problem species is resolved and having it flagged will be creating extra unnecessary ID work. We know that as IDs are fixed and the CV model is tinkered with, many problem species have been resolved.
Given the above, if my understanding is accurate, I would propose starting with a flagging system if that can be implemented faster, while waiting for an automated system to be developed. But there are a lot of things I don’t know about what happens behind the scenes that could change this. Long-term an automated process seems more sustainable and higher priority.