Shipping line items not displaying with [commerce-order:line-items]
If you enable the Token module (maybe you already have?), you are given a new view mode on all fieldable entity types called Tokens. You need to enable this in the Custom display settings fieldset on the Manage display page for order types (found under Administration > Store > Configuration > Order settings). Once you've done this, you'll be able to choose any eligible View you want for rendering the line item field's tokens, so if you add another display to the default View and remove that line item type filter, you can use that just for rendering the token.

You can read more w/ screenshots here: https://www.drupal.org/node/1299662