The issue here is how NCWest decides to put up information (or the lack of) in their patch notes... In game what you have is colors and names, let's call it ranks/grades: General (gray background), Advanced (green background) and Top-grade (red background) for each homunculus. So 5 different ones x 3 rank/grades.
This cannot be improved so far. You get korean random chance in the creation of the homunculus, and a General one cannot be upgraded / leveled / whatever you wanna call it to a Top-grade one.
Regarding the stages 1, 2, 3 for the Communing Abilities (slot machine), that table you have in the patch are only stats the General (gray background, lower grade pet). They are missing the tables with the stats for the Advanced and Top-grade homunculus. And the difference for a level 5 stage 3 general homunculus skills to a level 5 stage 3 top-grade homunculus stats are +20 or +2%, sure it isn't much, but that goes as everything else in this game. If you have a top-grade pet for your character class, it's best to invest on it. If not, you play with what you have not everyone can afford to spend vitality bars and 50bi SP every 24h.
BUT you cannot upgrade a General low level homunculus to a Top-grade one.