Plan A: There will be many runways where the escape route is obvious and can be selected as standard. Operators wishing to substantially comply with the standards set for each such runway will not be unduly penalised by following them if required. The airways clearance would automatically include a contingency for the standard s/e procedure. Operators will normally go for the standard, rather than have their flights delayed by a special contingency clearance .
PLAN B: If an operator wants to squeeze in the last kilogram of payload / fuel on a regular basis, and devises a s/e procedure that is better able to do this, it could be annotated on the flight plan. If this case, the departure clearance will include a provision for that.
For runways where the escape route is not so obvious and operators choose different s/e routes, see Plan B.