Shopify Amazon Shipstation Marketplace Connect Oh My

Ok, so here is the question. We have a shopify store and use the marketplace connect app to sync our listings to amazon. When those orders on amazon come through for Fulfilled by Seller (not prime) they come into shopify marketplace connect app and then those are synced to shipstation under the shopify store in shipstation. Once we ship, that information goes back to shopify marketplace connect and then updates amazon. Here is the question, should we not use that "process" and instead simply use the store connection directly to amazon to import the order and ship them? Pros vs Cons? We do have Amazon Buy Shipping connected as a carrier, but as I am writing this, I don't know if we can use that if the orders come through the shopify store process as described above. With all this said, we have the same exact setup for eBay, but eBay doesn't have so many strict rules, etc. So we don't see any issue there.