Dear Varganito,
I think its possible, i have tried it myself.
But what you could do is once an order is placed, the cost for customization can be added as an additional product into the catalog.. and under administration you can edit the order, and add this product into the existing order.
Once you have done that, you can under status tab for that order, update the status as per your need, and select notify customer.
You can also, ask the customer to conifrm the changes via email, the customer should be able to login to his account on your store and check his order and changes done to it ..
Hope this helps. You could try it and let me know..
I havent tried it.