But the question remains. Is there a more all inclusive resource for the Arduino's command set, memory management and eccentricities of C/C++ when used on a microcontroller?
Not that I'm aware of. There are a number of books available, but I haven't read any of them, so I can't recommend one. I do know that at least three of them were written by forum members, so hopefully they'll chime in and say something about their book in relationship to your question.
Attempting to learn this based on bits and pieces, clues and the occasional code snippet is slow going and results in a lot of code rewrite when a better way is discovered.
I can sympathize with that. But, that's about all I can do.