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I can give a simple explanation. The code for switching to 60 Hz is in every Katana Dreamcast game, because it's part of the SDK library. So it's just a matter of forcing the region or the code to be used via a patch.
For WinCE, it's most likely something that is coded directly. Ie. when they add a 50/60 Hz option into the game. Could be any number of ways to implement it, resulting in a different code sequence. Of course if it's not included, then the code is not in there at all. A similar story for CDDA patching.
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