Can I run a 12mm plenum spacer for 3.8L VY Ecotec with a stroker kit? Does it just have to be all tuned in or can the plenum spacer just suit a standard engine?

You can run a 12mm plenum spacer on an Ecotec stroker engine, without a tune, successfully. Given the increased engine capacity, the plenum spacer will work better on a stoker then it would on a standard Ecotec.