This feature was released in version 1.12 of Atom, implemented in Pull Request #120.
To enable it, checkmark the option labeled Add Known Words, found in Packages -> Settings View -> Open, or shortcut Cmd + ,. Then go to Packages tab and search for spell-check.
Then, to add a word to the builtin dictionary, press cmd-shift-: while the cursor is on the misspelled word and select the item named Add to Known Words.