If Microsoft hadn't been playing catch-up on Mac OS since 1984, Windows would still look like a jumped up command line interface.
Neither Civ3 nor Civ4 are models of the way a cross platform product should work with respect to mods.
Mac Civ3 breaks a lot of mods because its folder structure is very different from the Windows version of Civ3, and is *already* similar to the Civ4 structure. There's no point in changing Civ3 to look even more like Civ4.
Aspyr did attempt to write file path translations to allow mods to work. Sometimes this is successful - there are several mods shipped with Mac C3C that work fine. If we knew the rules that are used internally, we could probably put together a set of symbolic links that would assist mods that currently fail to find the files they need. But we don't!
In any case, please don't use Civ4 as a model of how to do it. Mac Civ4 breaks a heck of a lot of mods.
The Civ4 folder structure is *still* different from the Windows version. "C:\Documents and Settings\[UserName]\My Documents\My Games\Warlords" does not equal "/Users/[UserName]/Documents/Civilization IV Warlords".
Civ4 Modders assume their mods are running on Windows, and they can get details of the user's folder structure from the Windows Registry. The Windows Registry trick doesn't work at all on the Mac, of course. It doesn't even work all the time on Windows!
The Windows Registry issue is a minor problem you often have to resolve first when porting a Civ4 mod. But then you start on all the other incompatibility issues with Civ4 mods on a Mac - no custom DLL, Python v2.3 instead of 2.4, a different XML parser, Windows-only help files ....
Good luck with discussing release of the source code for either product with Aspyr!
(a) Aspyr don't have the right to give it to anyone else. Code ownership rests with Firaxis.
(b) You'd have to climb over the dead bodies of both Firaxis/Take2 and Aspyr to get your hands on the code they both spent years developing.