Hmm i watched the replay, and other replays of pencil. Overall his micro is decent, but not really exceptional, but vindi micro is pretty good. I am pretty sure he doesnt use stop micro but something different, I tried some stuff a while ago but couldnt really reproduce it. Anyway the way he does it only works on big numbers and you still need very good micro and timing for it, this is not something everyone can do (while massing flaks is).
Vindis own flaks in low numbers, but once you get like more than 5-6 flaks you wont be able to kill them easily anymore (without losing a vindi which is required in order to make the vindi worth it)
I dont believe higher flak cost will really be a problem for soviets, i've been using fast air bo's often last weeks and have seen some good counters to it (on big maps its useless anyway). Maybe with early bulfrogs or migs?