I totally agree that commissions structure should be added and it is in the nearest plans. I am talking about what we already have.
The nearest big improvement to our multi-vendor is to create an ability to send funds directly to vendor's account and this change will assume commissions structure. I cannot promise there will be manufacturer/vendor levels, but commissions will appear. Steadily we will enhance our multi-vendor solution, so it would meet more and more needs.
As for now, payments to vendors are calculated manually by admin, but admin has statistics of sales by vendor.
As for custom order email notifications, this is a great idea and part of it will be included into upcoming 5.2.
Finally, X-Cart is integrated with QB and Xero via Webgility services:
http://www.x-cart.com/extensions/addons?field_tags_tid[0]=13