Mac, Windows, and Linux all have different philosophies on how to handle data files associated with an application. This does make Aleph One development pretty challenging, as doing the right thing for each platform means we end up with convoluted code to find stuff at startup. The DOOM community usually handles this by making the "engine" (runs a scenario) and the "launcher" (shows a UI to pick your scenario, and tells the engine what to run) into separate projects, but no developer has stepped up to build a launcher.
If you want to add MML to your Marathon 2 game on a Mac, like 3371-Alpha is doing, you actually have four choices:
1. Run the bundled app, and put your MML inside the bundle as 3371-Alpha did. The downside is, you have to re-do your changes when you switch to a new version of the app.
2. Run the bundled app, and put your scripts inside [your home directory]/Library/Application Support/Marathon 2/MML. This sticks around when you update the app, but it's an obscure location and a hidden directory on more recent OS X releases.
3. Run the standalone Aleph One and download the Marathon 2 scenario files separately, with your custom MML in the scenario folder. This is how the Windows and Linux versions work, because there's no concept of a bundle there. (The Windows download of "Marathon 2" is literally just AlephOne.exe with a different icon and name, but on the Mac there are compiled-in changes to make the standalone bundle work better.)
4. Run Aleph One like in 3, but if you install MML in [your home directory]/Library/Application Support/AlephOne/MML, it will be used for every scenario you run. You can also install plugins here (in the "Plugins" folder instead of "MML") and they'll be loaded in every scenario. This is handy if you have generic things like cheats or custom HUDs that you use in multiple games.
For further reading, see File Locations
on the Aleph One wiki.