Not sure how France (or other countries) deals with ATZs but the separation that you need to achieve is determined, in part anyway, by the airspace class - for example in class D you don't separate IFR from VFR.
If you have two aircraft that need separating, you need to apply any one of the standard separations that work - ideally you pick the most efficient. Vertical is usually the easiest but half the fun is finding some other way that can get both aircraft climbing as quickly as possible.