No it's not a problem. Producers know that people at home often single dose their coffee, so I assume they consider that when producing a grinder (in fact most coffee shops that do pour over grind single doses as well). Maybe in some manuals it's written that you shouldn't let it run empty on very fine settings, but that's more to avoid warranty claims than because it would actually hurt your grinder and I assume they are referring to letting it run for minutes on end, which you probably shouldn't do. And why would you? The burrs in any case shouldn't touch each other at all, even on fine settings (or only at the flat part of the burrs, but certainly not the blades). I have yet to seen a grinder that was getting damaged due to the few seconds of running empty after your dose went through.