I hear you, Chris. Precisely, that was the reason why I asked the question in the first place. If the factory spec for instance would say that the hole is 9/16", then using a 9/16" drill bit would respect the original tolerance, I reason. But you are absolutely right. Unintentionally making this hole larger than what it is supposed to be could mess with the engine alignment. If nobody knows the proper size of the hole I will clean it out manually with a file, like you said, before I screw up a good inner transom plate.
On a different and somewhat personal note: I noticed in your profile that you are from Down Under. Are you still living in Australia or are you now living in the States and are from Australia originally? Just curious!