Sailcovers and rain
The purpose of a sailcover is too keep the sail protected from UV and wind chafe damage more than rainwater or dampness. Although newer sailcovers just happen to keep the sail dry, as the cover ages the water will penetrate the cover. A main flaked properly and covered is loose within the cover and enjoys circulation in the breeze, hence a covered wet main is less apt to mildew. The contrary is true with a jib, which when rolled tighlty on a furler enjoys less circulation, jibs wrapped wet on a furler will mildew more than a main will. If I were leaving a wet main for more than a day or so, I'd remove it from the rig and store it loosely ruffled in the cabin which will further reduce the chance of mildew staining the sail over a long period of time, or the few weeks you mention. It is much easier to take steps to prevent mildew than try to remove the stains. I happen to enjoy sailing in the rain when there is no apparent threat of thunder and lightning.