All internal testing has now completed - and we can gladly state that BizTalk Server 2009 works with Commerce Server, without issues or any special black magic required. This applies to both Commerce Server 2007 SP2 and Commerce Server 2009.
Hope this helps!
What about BizTalk Server 2010?
I tried it out and it looked compatible. See my blog post: msinnovations.wordpress.com/.../biztalk-2010-likely-compatible-with-commerce-server-2007-adapters