This isn't even something that comes newly from DDD really,the secret reports and some dialogue pretty much spell it out for you in KH2. The DDD 'twist' to me always felt like it was only supposed to be news to Sora, not to us.
There are hints in KH2, but I don't think it gets super blatant until Final Mix, when Roxas and Axel have a conversation about it. Then Days comes along and beats you over the head with it, with characters repeatedly saying they feel a certain way, only for someone else to immediately point out that's impossible.