I think you are overthinking things. I don't really understand what you are asking.. it seems to be "how to do I color like this?" Which would appear to be a straightforward question with an equally straightforward answer - you pick the colors you want.
It's just a blue palette with three variations - shadows, mid-tones, and highlights.
There are some additional variations within that to accommodate some of the details within the image. However essentially the image is built using one palette, then areas are altered for a second palette to lighten them up, then a third palette for highlights.
You can use blending modes and transparency to do that if you want.
But you can just as easily use a secondary or tertiary swatch group and fill objects with standard colors - no blending or transparency. (image above is all just solid colors).
You can also use things like Illustrator's Recolor Artwork, 2
Which method you choose is entirely up to you. There's nothing inherently wrong with any of them. There may be some considerations though.
If you are working in CMYK mode, blending and transparency can yield undesired results. So you may be better off using solid colors.
For me, I dislike using transparency and blending within Illustrator if it can be avoided. But that's merely my preference.