There are many other apps/plugins/systems that can be used with your ecommerce platform.
Magento/Shopify/BigCommerce have 1000's of apps available in their app stores and many sellers using Trade Runner also use these apps.
In most cases you can use Trade Runner and it will not impact these third party apps, but as there are so many, we cannot hope to test compatibility with them all.
We are unable to provide support for third party apps as there are so many of them.
We recommend installing Trade Runner and testing it with the other apps to verify the expected response.