If Lyonel Strong is the father of Rhaenyra’s sons in the draft where they are married, then it’s logical to think that Harwin Strong is the father of Rhaenyra’s sons in the published version where they are extremely close and Rhaenyra’s relationship with her husband Laenor is described as practically nonexistent. There is not any ambiguity about the paternity of Rhaenyra’s sons in Fire and Blood or any of the short novellas. It’s an open secret that Harwin is the father.
not really because theres multiple drafts. there was a lannister match too, there was another one too. but honestly, grrm likes to change his mind as well. also grrm does this thing with targaryens repeatedly where he makes them not look anything like their targaryen parent and then make them go through a lot in terms of not looking "valyrian enough" but makes them worthy in their skills and capability and their personage.
also, everyone knows that theyre laenor's. because theres a scene in the book during the green council where cole goee on this rant about things and then starts calling jace "laenor's son" and a "whore's son" and how easily he is discredited and unworthy of the throne because his dad is gay and his mother had a lot of relationships.
so, even the greens have always believed jace was laenor's son. the thing is that, its hard to acknowledge it when it benefits him politically and bloodwise, and discredits aegon. but then the greens discredit it when it comes to being "more valyrian with valyrian features" and being from "good parents" who arent debauched or homosexual in the eyes of the greens.
its also very normal to not look like your parents. i have two other siblings. we look nothing alike, we share a parent. i look like my godmother, my middle brother looks like his grandpa and my youngest brother looks the most like my grandmother. so looks have always been a hit or miss and especially with an inbred family, rhaenys being baratheon and aemma being an arryn and we have later descendants like robert arryn being brown haired when they have blonds up in the vale too, its a whole thing.