The way I see it is that in q3 there's often a incentive not to run- as this burns up a set of tyres... Personally, I wouLd say that teams are allowed an extra set of option tyres when they set 2 timed laps in a session. However, this woudn't be perfect either- as teams would just do a lap on an old, worn out set of tyres, just to get the extra set!
The equitable system would be to limit tyres for qualifying, but then have additional, new, sets only for use in the race!