It is an ongoing discussion but at the moment they are built on top of two different visual frameworks (both built using System.Windows.Forms though). We have some rather unique needs that their framework doesn't deal with yet...
Ah the every popular discussion up here at Microsoft. I would say that yes there is some overlap but each are optimized for particular tasks. I would say that if you have one, use it. If you can't do what you need to, then start investigating the other one.
Sorry if it wasn't clear but the concepts and technologies shown in the above prototypes are not going to be in BizTalk 2006.
The current Mapper (BizTalk 2006) is not standalone at the moment but it is something we are looking at for its follow up release. Feel free to contact me directly (eddie dot churchill at microsoft dot com) and I will be happy to put you in touch with the
folks working on that effort. They might be able to give you a better idea when a standalone version might be available.
Glad you like what you saw. There is a lot more but that was all we were allowed to show.