It is may analysis that the black window frame at the top is causing the difference.
Lightroom toning adjustments are somewhat non-linear, meaning the image content dictates how much things become lighter and darker. This is especially true of Whites, Highlights, Shadows, Darks and Clarity.
In this situation the window frame at the top is a dark object darker than anything in the rest of the image, so it keeps the darks from becomes as dark as if it wasn't there.
Effectively it means you cannot use the Shadows, Blacks or Clarity with this sequence of raw images because of the varying amounts of black. The amount of cloud shadowing on the image will also have some effect, especially for Clarity, but less so compared to very dark or very bright pixels.
For this sequence of images, the best thing to do is probably FIRST crop all the images the same so that no extraneous window frame is showing on any of them, THEN synchronize your white-balance and other non-color and non-tone-related adjustments--noise-reductions, sharpening, and THEN do an Export of all the frames to 16-bit TIFs with a ProPhotoRGB color profile. Reimport these into LR and do your toning and color adjustments. It is not enough to crop the raw images, because the toning adjustments always look at all the pixels including those outside the crop box, not just the visible pixels.
RAWs and TIFs don't act exactly the same as far as toning and colors but you might start with the raw toning and color settings synchronized to all the TIFs and see if there need to be any other adjustments. Here is an example of my doing this where the first column of images are your two raw files with identical settings, that makes the window-frame one lighter, and the second column being two cropped TIFs with the same adjustments synchronized across them and both having similar brightness. You will notice that the hill, especially the bottom-right corner, is a different brightness between the two raws but the same brightness between the two TIFs.
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I don't know what would cause the difference in color in the night shots, above, unless it is a slow drift caused by the camera sensor warming up with use and the high-ISO noise increasing and affecting some colors more than others. If you're seeing a slow drift then this is likely the situation. If you're seeing the color randomly change back and forth between different frames, then it is likely something else that I don't have a theory for.