I'm guessing this stuff is referring to cut content from the development of the original game, but if sephy and aerith were brother and sister and grew up together, sephy would have grown up to be a very different man. Ifalna is a kind person who would never approve of Hojo's experimentation on humans, so unless Hojo ..."breeded" Ifalna, she would never consent to have a baby with him. If Professor Gast, who was researching jenova by interviewing Ifalna and recording it, was made to be sephy's father, Hojo would have no reason to "help his son" unless it was for research. Ifalna would have tried to escape with her son too if she had one. If Sephy was an ancient, I'm sure the planet would tell him some truths about jenova or his mother when she died. But sephy only seems to speak with his "mother" (jenova) instead of the planet. so unless jenova can not only block holy, but the words of the planet, that probably wouldn't have worked... There's just too many things they would need to change to make it work...
Now, if the question is not referring to possible alternate scenarios that could have existed, then aerith and Ifalna obviously did encounter each other (for the first years of aerith's life), but i'm pretty sure sephy was taken away from his mother at birth. He was told his mother was Jenova and we have no idea what they told him about his father. As far as I know, Aerith doesn't know her father is Gast either. Sephy was being raised by Shinra, but aerith and her mother were on the run from them and in hiding. eventually, they were discovered. but instead of saying they were under shinra's care, I'd say they were more under shinra's observation. Sorry if i'm going off topic. I guess i don't quite understand the question...