Portlet links/toggle list items that are added by user scripts (using mw.util.addPortletLink) do not receive the padding other items in the list do because they do not have the class toggle-list-item.
Expected result:
Actual result:
This can be resolved with the CSS:
.toggle-list > ul > li { padding: 0.75em 0.875em }
Ideally, the menu should also make the text look the same for all items and items added using JavaScript should be shifted to the right so all the text aligns. The items added using JavaScript should also have the background effect applied when the mouse enters them or they are clicked on, but getting the padding right is the most important because it makes the links easier to press and makes them look a lot better.