Sounds like your EDI provider is rigid, and I would warn this may cause headaches. In my experience, while EDI is generally standardized, everyone has their own EDI recipe and this is where using a one-size fits all solution falls down. Your EDI integration is likely to process hopefully thousands of transactions over the course of a year so worth it to build in the foundations to make it robust. You have some options. One is to create a mapping in the middle between Netsuite and your EDI provider, but not sure if you will be able to do that. Another is to customize Netsuite, but what I would draw the line on is changing the way you manage your G/L based on your EDI provider. There are dozens to choose from.
I pulled my hair out over EDI and ended up just building my own. What I wanted was full control on a partner by partner basis with robust testability built in. Hence I deployed a VAN, created an REST API on AWS API Gateway, that accepts inputs, generates and validates the parcels against a specs, and sends them up to a VAN, and then use an Airflow instance to pull things from the VAN, perform error checks / audit / validation etc. I use a local database on an RDS instance to store all kinds of logging information and built the interface to that using Next.js. It's all built in Python/Node, and arguably overengineered for sure, but it's bulletproof, scales horizontally and when connecting with a new Trading partner, I can quickly and easily modify the system to meet any partners requirements using a real programming language, without plaguing the ERP with excessive overhead, so all the logic for connecting with trading partners is neatly contained in the API interface and because of that we can run automated tests etc.
Amortized over the tens of thousands of documents we exchange over the course of a year, the cost per document is less than a penny, but the control ,ease of use, and visibility is priceless. And I think it's a lot cheaper to run on a monthly basis. Development costs are likely pretty high depending on who you are, I was the developer on mine so it was all free right. :D