Wikipedia has a bit more info including a few links about the kernel. It also reminded me that there were other "odd" 64 bit XP versions:

Windows XP 64-Bit Edition for Itanium systems, Version 2002 - based on the XP codebase
Windows XP 64-Bit Edition, Version 2003 - Itanium as well, built off the Server 2003 codebase
Windows XP x64 edition - The version you are seeing, Server 2003 derived for 64 bit x86 processors

At the time, Microsoft bought into the whole Intel story that Itanium would be the PC migration path to 64 bit. They built up a big separation layer (WoW64 - Windows 32-bit On Windows 64-bit), and all of it just carried over into the x64 versions, even for Vista and 7.

Back to your kernel issues, I find it odd you see differences between Server 2008 and Vista. Those should be lined up code wise when the latest service packs are applied (or so I thought). And Server 2008 R2 is supposed to line up with Windows 7. Any odd differences in Windows 7 32 bit vs 64 bit that you are seeing in the testing? You could verify the actual kernel file is identical (C:\Windows\System32\ntoskrnl.exe) between Windows 7 64 bit and Windows Server 2008 R2. May not reveal subtle changes in how they run when in server or client mode, but would at least identify if they are the same binary.