How to get "empty line items" in Commerce, similar to Ubercart?
In Drupal Commerce, we made the decision to add line item type dependent callbacks to the line item API. A product line item will function differently from a shipping line item will function ... etc. As a side effect, this means there is no such thing as a "generic" line item, just like there is no such thing as a typeless node.

What needs to happen, if it doesn't already exist, is a small contrib module could be made that adds a basic line item type whose "line item add form" in the order edit page lets you specify all the information needed to manage and display that line item. Where it's gonna break down are things like pricing rules - should these line items have taxes? Should other discounts apply? Or display rules - should these show up on customer order pages?

There is no such feature in core (as you can see, it'd be a small contrib, but it wouldn't be trivial to make), but if it were tested and proved as a concept in contrib, I don't see why we couldn't consider it for inclusion in Commerce 2.x.