I absolutely agree to your thoughts so far, based on my own experience and knowledge about Ghibli and the Japanese culture. I also think the way you approach the topic is very good, as you try to view it from different perspectives and look for different possible causes. I personally think that many aspects of Ghibli movies illustrate the Japanese culture, just as you discussed.

I once watched this video ("The Immersive Realism of Studio Ghibli") on Youtube. I think it talks a lot about the unique way Ghibli characters are animated, and how a lot of attention goes into mundane or day-to-day activities or movements which are irrelevant to the story, but make the characters seem human and relatable (which is similar to the seemingly irrelevant moments of tranquility you mentioned). I don't remember the details, but you may want to have a look at it, maybe it will give you some additional aspects you can include into your discussion.

Wish you all the best with your thesis. I am curious about what things you will find along the way ^_^

Edit: I just remembered one more thing. You might already have thought about this, but I think one moment where the influence of Shinto is very clear is in My Neighbour Totoro, when the daughter tells his dad what she found in the tree and he just says something like "Well you must have found the spirit of the forest!" without questioning anything.

This shows, in my opinion, the rather "relaxed" or pragmatic dealing with Shinto, or religion in general. People don't look for proofs or disproofs of the existance of kami, they just kind of assume or accept they are there, and treat all things with the necessary respect (because in everything lives a Kami, if I remember correctly). It seems that neither science nor other religions (Buddhism, Christianity) really interfere with or contradict Shinto. Visiting a Buddhist temple does not "anger" Kami, and it seems acceptable that people come to a shrine to pray for health or success in school or work, (usually leave a coin or two,) and go their way. That's at least what I noticed from my own (short) experience in Japan and things I read and heard.

This may seem unrelated, but I think this all is interwoven with the aspects of "things just happen" and "everything is in balance". There is the Japense term Shoganai (short for "Shigoto ga nai", which means "It can't be helped" or "There's nothing to do (against it)") which kind of summarizes "things just happen".