A simple fix for all your HDR problems is to use the following process.
- Use your original photo, as the base layer.
- Place the generated HDR on top of the base layer.
- Mask out the imperfections.
- Be creative, try different layer styles to get desired effects.
The problems that will be fixed with this approach:
- Textures at unwanted places. Dark clouds
- Contrast depending upon the pp technique.