I would not mix everything together.
If there are special game modes for random maps, okay. But I would not add dynamical (or so called flexible) things to scenario or skrimish maps, because I think that every creator of a scenario/skrimish map had a particular plan/idea how the map should be played or what the challenge is. But, a modder should still have the possibility to create a special, good balanced scenario or skrimish map that is only playable in such a special game mode.