Generally speaking it is very surprising for a merchant of any product to require that you not use a competing product in order to use their product.
plugins, fulfillment, order tracking, the UI. it does way more than billing.
Any of those could be arranged with woocommerce / magento / shipstation.
If your SAAS wants to integrate with Shopify (which owns a majority of the market for SMBs e-com websites), telling your customers to switch to magento is a no-go.