Sometimes I create multichannel tracks for dolby digital to export to ac3 files. Then I have to choose “Use custom mix” (Preferences → Import/Export → When exporting tracks to an audio file).
Otherwise I often create stereo files for MP3 or wav files, so I have to choose “Always mix all tracks down to Stereo or Mono”.
It would be probably much easier to select this option in the export window.
If you want a mono file and you are set on “Use custom mix”, all you have to do is to mix the project down to mono before you export. The “custom mix” dialog will then default to making a mono file.
Similarly, if you want a stereo file, mix down to stereo before you export.
One advantage of mixing down before exporting, is that you can check the levels of the mix, and normalize if necessary.