> The reason for the 64-bit stuff in the System32 directory makes sense - they need to ensure that the currently-used DLLs and stuff are in the directory that legacy software is looking at.

Why? There was no legacy 64-bit software. So any software needing to find the 64-bit system directory needed to (at the very least) be recompiled, but probably needed lots of other small changes as well. So why couldn't one of those simple required changes (to create 64-bit versions of legacy software) be to change the path from which it loads its DLLs?