Strictly speaking this is true, but voter turnout is one of those "close is good enough" statistics. Sure we can't stop a voter from walking away with half their ballot, but we can at least provide a statistic that is close. We just need to let administrators know that it is an approximation. If they want an absolute stat, they can use cards cast and decide the turnout on their own. Obviously it needs to be an option.
There are several ways of handling this technically. One is the "minimum set" solution you mentioned. Another is to use some kind of statistics race. This solution seems to be used by other systems out there, and is what we're leaning towards at the moment.
I am not sure when this will be implemented, but it is highish on the list. We have not had many multi-card GEMS accounts up 'til now, but Puerto Rico is important enough to take the feature seriously. Stay tuned.