I don’t know when I made the comment about the first sun being in the Y-direction, but I don’t think that makes sense in this context. The output of gendaymtx is always dictated by the weather file, which delivers site coordinates and time/day information to determine solar angles.
The difference with and without the gendaymtx -5 option is significant, as you noted. This option was added at @Andrew_McNeil behest to put all the solar energy into one patch at a time rather than distributing it over the nearest four patches. It also uses the actually solar solid angle to compute luminance rather than patch size. The addition of the -d option removes flux from the other (non-solar) patches.
Bottom line, I agree with Sarith that this is the command you should be using to compute the solar-direct portion of the 5-phase method, but other users understand the details much better than I do at this point. For example, @David_Geisler-Morod1 figured out a way to include specular reflected components more accurately in the 5-phase method. See alsothe related thread here.