Normally, you should use a sales quote for this. That transaction entry form even has the ability to change the title to something like Pro Forma Invoice. Sales quotes also have no financial impact. The reasoning is that a sales quote is an outgoing document, while a sales order is internal and represents an incoming order, which you have not yet received at the point in the workflow you are describing.
Just add the new line. Freight is definitely not an inventory item, because it is a service, and has no value until the service is performed.
Why would you pay in advance for everything? Deposits are one thing. Full payment is pretty unusual. Maybe you need to find new suppliers. After all, you’re the customer. Legally, it is the invoice that creates the obligation, not a quote.
Again, definitely not an inventory item for a service. For incoming freight on purchased inventory, you don’t have to create anything. Read the link I already sent about Freight-in.