When I was raising Tilapia... the seller addressed runts, 1st they culled for them, so I wasn't supposed to get them... I still did on occasion, but maybe 1%, and they didn't live long in a farming tank.. they said it often happens, when the fry don't get all the want to eat, multiple times a day... so if you were just feeding a little more than they could eat, and sucking up the rest, then feeding 6-7 times a day... you would likely have less runt issues than feeding them an amount they could eat in 10 minutes, 2 to 3 times a day...
also any accumulation of hormones could be a cause as well... bigger tanks are a plus, as well as more frequent water changes...
all this assumes they are correct genetically... the more line bred / inbred they are, one would assume the more actual genic issues you could have... our indoor dog, is / was a runt, and we were concerned he would have health issues associated with his "runtiness" he's been a good dog so far, but there are no guarantees, when you start out