Users can already specify custom subdirectories in their package.json files for stylesheets, keymaps, menus, and snippets. Atom falls back to wisely-named defaults so listing these paths aren’t necessary (but useful for users who want a bit more control over their codebase’s structure).
Should the grammar and settings folders not work in a similar fashion? A user† may be bundling a language grammar as an auxiliary component for something much bigger, and having these two extra folders in the root directory (because they can’t be overridden) just adds to clutter.
A snoop through Atom’s source shows the grammars directory is hardcoded, whereas the other paths first check for config options first…
† - I’m currently that guy, and I’d rather not sunder my package into two smaller ones for the purpose of keeping clutter out of the base directory.