Not chocobits, but personally they look like something like this in my mind. It’s a diagram of what qualify what. The higher you go, the closer to the main clause you get, with the main verb at the top.
本を読みました
それはかれの赤い鉛筆です
それが決して難しくは無いんです
それが決して難しくは無いんです (variant)
故郷の駅で外した鼻ピアス
故郷の駅で外した鼻ピアス (variant)
One thing I miss in your sentence diagram is that they don’t show the head-final left branching nature of Japanese. It’s was a big epiphany for me when I realized at some point that a word can never ever qualify what’s before it (with some caveat, like inversion in casual speech). But I’m not a beginner anymore, so it’s hard to know what’s the most useful for them.
Ans also, yeah in the end there are always a tons of difficult details at the tactical level, like how to treat topics marked by は, should we try to always explicit invisible が, how to deal with stuff like 難しはない or んです… This is hard and I’m not sure what’s best.