There is no clear cut answer to which is best. Personally, I'm always recording 4 channels with this recorder and I find myself switching between using stereo x 2 and mono x 4.
A practical advantage of stereo x 2 is that it writes two interleaved stereo WAV files, one for each channel pair, and those files may be listened in stereo directly with most any WAV capable software or hardware media player. To listen to mono files in stereo you must load them into editing software or combine them into an interleaved stereo file with something like WaveAgent first.
Plus, since we are most often dealing in stereo pairs, for file management and quick listening to the raw files I find it useful to have one stereo file for the AUD mics and another for the SBD, or whatever the pairings are.
However, writing individual mono files doubles the record time between 2GB file splilts which might be useful. The time at which that split occurs is determined by the record sample rate and bit depth.
1x4ch keeps all the channels together in one file, which I suppose may be useful. I never used that one myself as it files splits too frequently while recording and I can't play the raw files easily without loading DAW software.