The washing out is a side effect of local contrast enhancement or tone mapping. See @agriggio’s. I spent too much time on the panorama so I let that go.
As for global contrast, yes – it would benefit the image creatively.
The amazing thing is that I didn’t do any explicit smoothing whatsoever! I just kept a close eye on noise as I processed the image. Bad pixel interpolation and resizing, and using the brightest photos, may have helped but everyone does the first two.
Avoiding one-click solutions where I can (nothing wrong with those) and using the power of math, stats and friendship 
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I didn’t use all 9 photos, only the 3 brightest and disabled clipping.
I don’t remove hot pixels or clip negative values in PF. I deal with them in G’MIC where I can use math, stats and extreme pixel peeping to determine which strategies are best. @heckflosse
I took the linear TIFs from PF, brightened and saved copies of them, creating artificial bracketed sets of 2. After brightening, the sky is perceptively featureless.
No. I merely maximized the weight to favour contrast. In retrospect, the previous step did that for me
Alpha is just another channel, which you could delete using any app including GIMP. enfuse and hugin use and export it. The reason I remove alpha is that I don’t need transparency or masking.
Yes, it is a terminal app. I talked about it in another thread. Just search the forums.
Chroma is the C component of LCH, which is the polar projection of LAB. You could modify it in GIMP, RT, dt, etc.
No problem. Clearly, my process is atypical. No other raw player does it this way, probably because it is a time waster. I would advise against it.