It's not unreasonable that they simply changed color upon changing form, while others don't. The Toa Inika did this, as did Kopeke when he was rebuilt, and Hafu & Ahkmou when they were diminished, and Nuhrii at some point in-between, but not all Matoran or Toa change colors every time, as seen with the Toa Metru's transformation into Toa, or most Matoran between 04/01/03.
There's no mention of the Matoran having become lighter due to the sun even though those we saw on Metru Nui also for the most part had Metru colors as opposed to Mata colors (including Metru brown, which is lighter than Mata brown. We also see Metru blue on Mata Nui). Only thing that was mentioned was that the sun caused the silver paint present on the powerless masks to fade (qnd the likely originally present black paint on the noble masks brought from the Great Temple and later retrieved by the Toa Mata).