2. Autogen appears only where it is defined in OSM data, where I think WT gets the autogen data. All these areas needs to be defined manually first there, so if it's not there it won't show up in WT either.
3. I also had / have problems with lakes, where part of them are simply black or the shoreline is not correct. It happens where the watermask layer is not correctly set for the photoscenery above it. Where the watermask does not contain water (so when an area is not defined as water) FSX / P3D simply won't put water in and you will see the satellite image of the lake / river (which you call "white mask"). Hope it will be fixed or improved in future versions.
4. About clouds on the image there is nothing to do sadly. At some (less popular or more remote) areas even Google has textures with coulds.