Another thing detracting credibility from your theory is that not only is the head-shape thing not shown to be hereditary in-universe, but Phineas Flynn and Heinz Doofenshmirtz also have different variants of head shape. Phineas, for example, has a long pointy nose, while Heinz has his chin as the point of his triangular skull. With such wild anatomical differences, it's a miracle they're even the same species (actually, legally speaking, they're not!).
I'd also argue that though Phineas and Heinz both seem to be master engineers, that's maybe the only quality that the two share. Heinz is a classic screwball with a fractured childhood, unconventional relationships with others, and deep, unresolved animosity. Phineas is a curious, inventive, optimistic boy for whom life seems to be a world of pleasure - he's rarely ever seriously upset at anything.