Atom and VS Code listen to your .gitignore when showing a folder of files. Quick searches ignore those files as well. In Atom those folders/files are still openable (the explorer pane thingy shows them as grayed out).

To get the same functionality in Sublime, AFAIK, you have to create a couple of project files first and add folders into it. Then, if you later make a new folder via the terminal you have to edit your project file to include it.

That's been my biggest headache around Sublime vs. Atom. It's the smallest thing but it's like sand in my shoe.