The rules for Badgegen badges and belts are defined here:
It is true that the rule regarding belt points for gemstone badges says "1 point per gemstone badge (excluding country badges)" is open to interpretation. One interpretation is to say that you have one gemstone bagde when you get to ruby, two when you get to saphire and so forth. I am guessing that project-gc either has consulted the author of Badgegen to have him clarify the rule or just simply have chosen to implement it to behave the same way that the Badgegen makro for GSAK does. Either way, the interpretation seems to be that badges supplant previous badges so that the only time you get a belt point for a badge is when ruby is achieved.