It honestly doesn't matter. It can be less messy to do it in the bowl as any dough residue stays contained. However, some people like to tip the dough out on the counter. It's important not to flour the surface when you are performing stretch and folds as this will alter the hydration of your dough. Lightly wetting your fingers (and the counter top) can help - but again, be careful not to use too much water as this will also alter the hydration of your dough.