Question: How do I clearly mark and label "To-Do"s directly in my code (using Atom on Mac) for later?

Answer: 
I'd just mark your comments with `# TODO`. Most IDEs have a way of aggregating these comments to a list. Atom is no different, although you'd need to install [a plugin for it](https://atom.io/packages/todo-show).
This doesn't strictly satisfy your requirement of not using comments, but most IDEs support "Todos". Just start a comment with "todo":

```
# TODO: Fix this code!

```

In many IDEs, this will cause the comment to be marked in some bright color (light blue in IntelliJ), and put it into a TODO section so it can be viewed later. This can also affects things like Git commits. I'm warned if I try to commit code that contains a TODO.