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There are times when a table explains things so much better than just text.
From BizTalk Server 64-Bit Support:
Which versions of 64-bit Windows are supported?
All versions of BizTalk Server 2006 support 32-bit execution on Windows Server 2003 x64 (including R2) and Windows XP Professional x64 by using WOW64. Additionally, BizTalk Server 2006 Enterprise, Developer, Branch, and Evaluation Editions support native 64-bit execution on Windows Server 2003 x64 (including R2) and Windows XP Professional x64 by installing both 32-bit and 64-bit executables and providing configuration options to use either 32-bit or 64-bit modes.
which means:
32-bit execution by using WOW64
Native 64-bit execution
on Windows Server 2003 x64 (including R2) and Windows XP Professional x64
Here's the justification (that I've borrowed from an official response on one of Microsoft's forums):
"We consider 64-bit support an Enterprise Edition level feature that a customer would only select if they require faster messaging/orchestration processing or the larger addressable virtual memory of 64-bit mode for large BizTalk message mapping or other memory intensive operations. Because the Standard Edition is designed for small-to-medium environments, it is licensed to only run on a single BizTalk server with a maximum of two CPUs, maximum of five "BizTalk Applications", and a single message box. 64-bit support for the Standard Edition seemed counter-intuitive from a technical and licensing perspective. If the deployment scenario requires 64-bit hardware then it certainly requires BizTalk Enterprise as well. Standard edition is for single box only installations. Enterprise is also required for multi-box installs and for clustering."