So if you went to do a half depth stop for a 25m dive, would you stay 3mins at 12m in addition to a stop at 6m?
I can't speak for Mares, but circa 2008 with a Suunto, the deep stop only kicked in well beyond recreational limits. Even when there was decompression it was still unlikely there'd be a deep stop. We did a swag of 20min 42-44m dives with no deep stop. We did a 10min 60m dive and the first stop was around the 30m mark for 1min. I think the next stop was 18m, then 12m, pretty standard after the deep stop.
To the OPs point, I'd use standard deco stop signals previously described. The deep stop is inarguably a deco stop, the entire theory behind them is about off-gassing. Signal we go up to a level, signal the depth, signal the time. Definitely rethink why you would want to stop deep, the research is pretty clear that the theoretical benefits aren't realised and it's best to get shallower.