I prefer the first version since, as you say, it's less noisy. For the same reason, I'd remove all the little bits of dark cloud and focus on larger forms. Chonky Pixel has a really good post about drawing clouds here:
https://pixelation.org/index.php?topic=48706.msg230771#msg230771Wherever I've deviated from his advice is just due to my own inexperience and the image dimensions.
I've done a quick edit with what I hope is the correct palette (I'm not familiar with Sega systems but I got it from a Sega fansite).
There are plenty of images on Google but I particularly referenced these two:
There's a lot of detail in these images but, at the scale of your image, I think it's better to strip most of it out and apply the most general elements. It's also helpful for the background to be less cluttered so it doesn't make the foreground harder to read, and this is very important in a game since players need to know which elements they can interact with. At the full Mega Drive resolution, you could probably emulate the exact cloud forms much more closely without them becoming too busy.
You can see in the references that the top of the clouds aren't super dark (appearing more that way because of the contrast with the brightly lit parts). I made the top purple (based more on the first reference and other images I found), which also lets this particular cloud stand out against the dark blue of the rest of the cloud cover.
I struggled with the holes in the cloud. I don't think they're very easy to suggest at this size, but my intention was to have them appear in horizontal strips, with the tops being flatter (as they're also the bases of other clouds) and the top being filled in with the bubble shapes of the top of the clouds that are further away. On a larger scale, I think that would suggest dense cloud cover against the blue of the sky.