This is a request for a very Useful feature that can be used at the Integrated Stores Setup level.
Right now the "Custom Fields" on the order are not mapped to any of the fields from the Integrated Stores.
Custom fields are a powerful way to set up RULES, therefore making them available can tremendously expand the way imported orders are automated.
My suggestion is that at the setup level of each Store to add a drop down menu for "Custom Field 1, Custom Field 2, Custom Field 3" where you can select which fields from the Store Feed you want mapped to these fields.
This can be a very powerful feature as each user can optionally map fields to the import that are important/relevant to them and use RULES to further automate the process