Yes. When they were producing the Mac versions there were no updates around for the Windows version, so they didn't notice that the menu option did the wrong thing. That's their excuse, anyway 

Alan, any ETA on a new version of the HOF mod?
Please note, though, that I have not explored whether it's possible to spilt the ~/Documents/ folders to make one for each version. Unless you find a way to do this, they will both share your ~/Documents/Civilization IV/ folder, where your Saves and .ini file live. Your Civ4 settings will therefore apply to both, and autosaves from one will be overwritten by games played in the other.
Sure, you could patch it manually if you had all the files. You *might* be able to extract them from the patch installer using a piece of software called Pacifist.
6. Make a copy of your working Civ4 v1.61 folder and move the contents of the extracted AspyrLinkToGameFolder folder into it, using the following recursive procedure. I'll call the folder hierarchy within AspyrLinkToGameFolder the "Source Tree" and the folder hierarchy within your Civ4 folder the "Target Tree".
That would work, but it would be a bit labour intensive, and might be error-prone. I guess you could create two workflows, one for each version. Each one would do the relevant folder renames and launch the relevant copy of Civ4.
Well, its a very long and tedious process, but manually patching works fine, no difficulties at all, and no mysterious files either.
Civ 4 is running great~