Mentioned many times on Hacker News, but very relevant here: https://eater.net/. A great way to understand what's going on by building a computer from the ground up.
I experienced a little shell shock reading this post. I ran into all of these problems (and more) while building an interactive editor in VR. Selecting things across the "180th meridian", grouping them, aligning them, distributing them, etc.
"First, we developed a process that effectively unpacks equations, laying them out in a branching, treelike structure..." Umm...like an expression tree, perhaps? https://www.geeksforgeeks.org/expression-tree/