I assume you do not have the City version, thus have the strap that goes over the top. If you have not thought of this yet, I store my rain gear on top of my front loaders under those straps.
When it starts raining, I do not want delays getting my raingear out and I certainly do not want to have my waterproof bags open catching rain when I am getting my raingear on.
I usually fill my front loaders. If they are part empty, the straps might not hold stuff on very well. In that situation, rain gear inside the panniers makes more sense.