I can't think of a circumstance where you would have folders in an override folder, so, no.

For example, you will have a includes/languages/custom folder, and an includes/languages/english/custom folder.

But you would have an includes/languages/english/html_includes/custom folder, not includes/languages/english/custom/html_includes

You really can't go wrong by creating a 'custom' folder everywhere you find a 'classic' folder and at the same level.