You can ignore the installer warning. It will install anyway. It runs fine, I am running MC 6 on a Mac Pro 2,1. That machine (and the Mac Pro 1,1) have 32 bit EFI, as you noted. Mine is a custom configured 8 core.
MC still runs in 64 bit mode. The OS cannot run 64 bit kernel extensions, but that doesn’t matter unless you have DX hardware. The new DX kexts are 64 bit only, I have heard.
Note, this is an unsupported configuration. But it does work. make sure you max out the RAM if you want it to work well.