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With Suunto computers, if you already did a complete stop and then went down again but stayed shallower than 12 meters, it won't tell you to do a safety-stop again. In regards to the computer saying that you did a stop, it won't says so clearly but it will show your profile underwater when you download the log including the time and depth for your safety stop without being explicit stating that it was a safety stop.
And not all of them are configurable either. I do 5-minute safety stops, not 3. Those two extra minutes keep me alert for the rest of the day and if my PDC doesn't support that, I simply check the time and mentally add five more minutes to it. Not a tough task at 15 ft.My ancient Uwatec Aladin does not even has safety stop countdown!