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The layouts are similar, but not the same. MacPython-OS9 uses the source tree layout, and Windows-Python too, IIRC.
MacPython-OSX in a framework build uses a normal layout, but in a very funny place, with lots of symlinks to make it behave like a framework. I would be very surprised if, say WinCE python or AS/400 python had anything resembling a unix layout. But all these layouts are similar enough that I've never come across a Python where I felt completely lost.

I think there's nothing wrong with enabling people to use their preferred layout, if they have a good reason for it, but I would be against enforcing it unless the advantages are clear and universal.

And someone has to do the work:-)