In the Golden Age, CBM and maybe Ross had flat bottom bunkers. MacKenzie, Tillie, Colt, Flynn and a lot of others (i.e. the white faces of Merion) used flash bunkers. Tillie seemed to have the most variety. MacK seems to have the most fans now of aesthetics. And, I think the biggest reason for flashed bunkers then and now is that, to quote Billy Crystal, "They look mahvelous, dahling".
I agree that early gca's in fact seemed to do trench bunkers but most "grew out of it" for more natural looking styles.
I am not sure that either style is particularly more penal. Each can vary in depth, ball location, etc. to produce mostly playable shots, but occaisionally, a very tough lie.