In my experience, different numbers are common for purchase orders (where you typically use the supplier’s number to make sure you get what you want) and inventory (where your concern is counting, managing, and using the right item). We always included notes on various supply sources, equivalent parts, and different suppliers’ stock numbers so we had flexibility when we needed to order.
Sales invoices are another matter. Sometimes, you have to invoice for the customer’s number, sometimes for your own. Sometimes, you are invoicing for a “kit” that you never purchased in its entirety, only as piece parts. Sometimes you invoice not for an inventory number but by referencing a contract.
I don’t think there is an easy way around this, no matter what accounting package you use. My attitude has always been that as long as I can send out a sales invoice, I don’t really care how hard it is to generate.