As moderator I deleted several replies to this message. We are going to have a do over here.
First - a reminder to all that bumping up a discussion is typically frowned upon. If the issue is still a problem, add a comment indicating what you have done, what further research you have tried, what things you have ruled out, etc... We assume that if this is a current, ongoing problem, you are working daily to resolve it so there must be something to add.
Pavel - you may not have gotten any responses because maybe the question wasn't clear. It could also be that there is no one here with experience in the area you are looking at. I'm not that familiar with the integration of QM to external WMS.
Out of everything you wrote, I gather that your real question is "The IDoc handling will be done via XI, so how to trigger output message from R/3? ".
That really wouldn't be a QM question but more a development or BASIS question I think. That part of the process is pretty much totally outside of the QM module I think. But maybe I'm not getting your question.
Craig