Did you ever figure this out? I too would like the ability to generate invoices with the eCommerce Addon

If you enable "default gateway" in addition to your chosen payment gateway, e.g. Paypal, this allows you to take an order via cart and checkout which adds a "Pending" order but does not require payment there and then.

I have changed some of the text/button messages for the Default Gateway option to read "Request invoice" or similar (the standard messages have instructions such as "Pay using Default Gateway").

It is a challenge to track down the location of each message but you will get there in the end.

Once completed, it is the a perfect "Invoice" option.