Muting all regions on a track (instead of muting the track) will make Logic disregard that track in the export.
Atleast this works for me.
"Export all tracks as audio files" does not separate mono and stereo, if there are both kinds in your project. All files become stereo. A way around this is to make two exports. First all stereo-tracks and then all mono-tracks.
To get the mono-export right though you need to make sure all stereo-regions are muted (I mute all the tracks also just to be sure) and that all mono-tracks are actually in mono. Doesn't work if there are stereo plug-ins on the track (should be a single-ring underneath the fader). Also you need to switch the main output to mono by hitting the double-ring underneath the fader so i turns into a single-ring. Hope this helps. Good luck!