That is true, though the differences were given enough focus to be shown right down to their aesthetics of ice and fire, which both fit well with their personalities. Nothing too grand in the big scheme of things, but still more attention than most Shonen tend to offer.
I'd still say the ending was far better than the alternative of it concluding on Dio's castle, since it was a decent twist rather than the typical case of a conflict ending with the climactic duel, offered some level of catharsis to both characters and made it so that needlessly continuing a character's story wouldn't be the case as it is in most Shonen after a protagonist has done all they needed (eg. Dragon Ball). I'd say Part 3 retconning certain pieces of information is more of a flaw to Part 3's writing than to Part 1's ending.