I have run some test to see whenever I can spot the source of the error. I run the radiation in ladybug, honeybee, and to check the gencomualtivesky I also run it in DIVA. I test it for both the original tokyo file I provided, and also the one you modified to match the integer numbers as per default, as per this post
The results are shown in the picture below
The deviation in the radiation analysis with gencomulativesky of honeybee legacy it appears to be quite visible.
Based on what I read and what I understood, gencomulative sky and gendaymtx are using the perez sky to generate the sky vault. This means that they both use DNI, DHI plus latitude and longitude.
So, what it differs, and maybe it is here that I am confused, is that while in gencomulativesky the sun position is approximated, in gendaymtx the sun position is exact.
Also something that I could not find is which sky model gencomulativesky and gendaymtx in honeybee-ladybug are usign: Tregenza or Reinhart or else.
If you could clarify this would be fantastic.
Thanks again for the fantastic tool!