I have a reference ID on invoices that is different from my transaction reference (or sales receipt number) that needs to be tracked in a custom field.

Add a field(s) for custom fields in QBO that you can connect with Dext

QBO custom field integration

Quickbooks Online Advanced allows you to add custom fields to invoices, sales receipts, purchase orders, expenses, bills etc. I would like Dext to be able to post to these custom fields.

You Import lists from QBO now (ie. Classes). - You should be able to import the custom fields as well.