I think if you take any set of symbols and map each one to a unique binary sequence, you can then structure it as a binary tree.
In other words Morse didn't have to be designed as a tree. The tree is just a data structure that fits any similar abstraction. You could probably do something similar with a multidimensional array (5D to include punctuation) but that's much harder to illustrate.
Well, you only got 2 symbols, so binary, and you want to minimize the symbols used for the whole alphabet+numbers. That naturally will give you a binary tree.
This is also an extremely difficult way to learn Morse code. No one that actually knows Morse code will ever use a chart like this in their thinking and listening pattern.
You're right, and your post needs to be seen more. Learn Morse audibly, not visually. Whenever I see someone post about these charts it instantly tells me that they don't actually use Morse.
Learning Morse visually means you have to decode it with more steps:
hear code --> visualise the sound --> decode to letter
Decoding by ear is the fastest way, and is the way that Morse operators decode it (eventually you just hear words).
I understand why the period is a 6-sound sequence (the complexity is organized by how common the character is in use), but it bothers me that it isn't just a single "dit".
So most of the symbols on the bottom are not on the chart st the top. However, the period is listed at dot dash dot dash dot dash, but the chart would make it dash dash dash dot.