It does matter, because these games were originally written for System 7, which supported data structures modern OSes don't called resource forks, which contain important things like sound and graphics and will disappear if you try to extract them on a modern filesystem.
The 79 MB versions you are seeing probably have textures and stuff from the XBLA release. The walls and scenery are OK, but definitely turn off the faux-HD monsters and weapons if you use this.
For the originals, go to
http://trilogyrelease.bungie.org . There you will still find four different Marathon 2's:
• The original Mac version (28.8 MB or separate files), which you don't want unless you're running the original executable in an emluator.
• The SDL version (28.9 MB), which is the above files converted to work with Aleph One
• I don't know what the 25.9 MB unimap is all about
• The original Windows version (87 MB complete or 7 MB for just the Map file), which has some minor differences since it was released a few months later, and not just to Waterloo Waterpark as the text says. Mostly minor improvements, but some people don't like how they replaced the alien teleporter on level three with an explorable roof over the building.