A very welcome news, today. The BizTalk team released to public an hotfix to let BizTalk projects (.btproj) to compile successfully under TeamBuild 2010 (http://support.microsoft.com/kb/2406405).
I discovered the issues myself and worked with the team to find some workaround. I am already using this fix in our project and I have been able to remove my own hacks.
You can find more details on bharry's blog.
Beware: this patch allows Team Foundation Server 2010 to build BizTalk 2009 projects. For developing you still need to use Visual Studio 2008 SP1 plus the Update for Microsoft Visual Studio 2010 Lab Management.