For very long recordings / recordings made at high sampling rates, a file that combines multiple tracks will reach 2 GB sooner than a group of single-channel files would do. Some audio software has 2 GB as the limit for any one file, so that can be a consideration.
Other than that, though, it's your free choice, based on your particular editing software and how it handles sound files. The way you group your tracks will matter mainly to the software operations that you intend or expect to carry out, so think ahead to that situation, and that should tell you what choices are best.
For example, for operas that I used to record in a gloomy old wonderful sounding downtown church that we're unfortunately no longer allowed to use, I flew a main stereo pair of microphones from a central overhead location, and put two spot mikes spaced very widely apart on stage. I recorded the signals from the main stereo pair as a two-channel WAV file. The signals from the spot mikes needed to be "panned" into positions some fraction of the way between center and left or center and right respectively.
For my particular software (Adobe "Audition"), in order to do that panning, it would have been most convenient to record the spot tracks as two separate, mono WAV files. However, the R-44 doesn't offer that choice, so I recorded them as a (second) combined, two-channel WAV file, then split that into two separate tracks in Audition. So the eventual multi-channel mix was made from one stereo file and two mono files.
The combined four-channel WAV format is one that I've frankly never used or even tried. A lot of software can't open WAV files with more than two channels, and while recording, the file would run up against the 2 GB threshold twice as soon as a pair of two-channel files.
--best regards