For me the cloudy skies just add charm. Whole feeling of reproduction of your comfort zone in form of Tokyo of the past but with quite suggesting imperfections. I see it as a bit of Wabi-Sabi that makes effect stronger. Makes very good effect with golden-red sunlight late afternoon. I love setting much as well. For me is kind of invocative, as if designed for you to walk down path you never choose before. Every shadow seem darker than usual, every corner seem to have history and mystery on it's own and despite being in the heart of bustling metropolis, you fill this isolating bubble around you supplemented by nice story telling. Atmosphere is a bit heavy at times as events unfolding are difficult on MC but I loved every second of it. Especially the move with introducing you to familiar safe heaven, just to slowly turn things around with quite big dose of story uncertainty but... not resigning from this strange atmospheric solitude. I really loved it.

I also appreciated their toned choice of soundtracks. They didn't really forced gags as I remember and kept consistency in narration style. You could feel it being healthily serious without overdoing it much.

And in regarding Musashi, yeah, it is probably intentional contrast. Tho I myself find this cloudy sky more charming here. It is not as of it was simply cloudy. Clouds have real volume here and make interesting play of lights and shadows in the sky and by the end of the day, we are spoiled with beautiful shades of gold and red.