Is there a way to script adding an item (in this case a markup item) on every invoice and add it to the last line?

yes, you just need to write a user event script for that - the script will check if the item already exists and, if not, will add it on either

beforeSubmit

or

afterSubmit

thanks!

I'd recommend doing this in a background script unless it really must happen in real time at the moment the user saves the invoice.

If you use a user event, do this in beforeSubmit, otherwise you are doubling up on database saves