It would help others answer your questions if you could be more specific about what you are looking to achieve in trying to integrate AS/400 with BizTalk. The limitations that you are seeking are not officially documented and would only be encountered when trying to implement such an integration scenario.
BizTalk adapters for Hostsystems comes with Biztalk 2006 will help to connect to AS/400 using MQSC/DB2 adapters. I don’t know much on limitations. I hope this link will help you