I'm no expert of Harmony so I couldn't explain the difference between the 2 approach unfortunately but this line does work for me :

from ToonBoom import harmony

harmony.session().project.scene.clipboard.paste_template_into_group("C:\\my\\super\\path\\towards\\the\\template.tpl", 1,"Top") # (beware, the double backslashes are mandatory if you are on windows)

Hope this is helpful