Ah I've managed to work it out and since there are no other answers yet, I thought I might as well post my solution here in case anyone else is interested.
So basically, in the "Add custom shortcut" command section I had to type "tomboy --new-note" rather than just "tomboy".
If you are not aware of certain command options supported by a program, you can simply type in your terminal "[program name] --help" and it will list them all out for you.
user@laptop:~$ tomboy --help
Tomboy: A simple, easy to use desktop note-taking application.
Copyright © 2004-2007 Alex Graveley
Copyright © 2004-2017 Others
--version Print version information.
--help Print this usage message.
--note-path [path] Load/store note data in this directory.
--search [text] Open the search all notes window with the search text.
--new-note Create and display a new note.
--new-note [title] Create and display a new note, with a title.
--open-note [title/url] Display the existing note matching title.
--start-here Display the 'Start Here' note.
--highlight-search [text] Search and highlight text in the opened note.
--addin:html-export-all [path] Exports all notes to HTML in the given location.
--addin:html-export-all-quit [path] Exports all notes to HTML in the given location and then quits.