For Malagasy species, it has to primarily do with range within Madagascar and IUCN Red List status. If they are only found within protected areas, they can not be legally collected, and thus have a zero quota (example: Calumma ambreense). If they are assessed on the IUCN Red List as either Endangered or Critically Endangered, they are given a zero quota (example: Furcifer balteatus and Brookesia decaryi). So Calumma parsonii is assessed as Near Threatened and has a large range that includes both protected and unprotected areas, so it has a quota. Brookesia perarmata, on the other hand, is classified as Endangered, but also listed on CITES Appendix I, so no commercial trade is permitted in the species anyway.
Those criteria cover most Malagasy species, although a few additional species do not currently have quotas either because there is concern about differentiating them from other protected species, or other reasons. I believe the concern with B. vadoni is that they are found in the areas that are most prone to illegal rosewood harvesting, and they are trying to prevent any collection in these areas to combat that.
Chris