It doesn't help that Remake makes several references to the OG either :p
I didn't feel it that way at all, neither from her GS speech, neither from Remake. I don't feel that it has to do with it, although there are slight differences between the two. In the OG, Aerith mentions this not because of Tifa, but because she knows that they cannot build a true relationship when he's not himself. She doesn't know him, so she doesn't know his feelings for Tifa at all there, she is speaking for herself and for Cloud, because she feels that something is wrong with him and he needs to resolve it before being able to be with someone. For the player, it's a hint at what's to come.
In Remake, it's different because she has understood Cloud and Tifa's relationship by the time this scene happens; she knows that not only it's not possible to build a true relationship with how messed up he is, but also that he does love someone else. So instead of telling him she wants to meet the real him, she warns him and herself to not fall for each other. IMHO, her warning was not only for Cloud (and the player), but also for herself. The situation is way too messy and difficult to handle. Usually girls prefer to walk out from such situations because it's a one-way to become heartbroken. Especially since I think Aerith has guessed that they will become an item. But I don't think it's about fairness; rather it's about recognising that once he'll be himself again, his heart will be filled by another girl. This is why she tells him it's "his imagination". Every time I see that scene, I know cleriths love it and I'm grateful they do, but I feel doom for Aerith and clerith. Hearing how it's all his imagination is hard. It's her telling him that those feelings aren't true and will disappear, that his fake persona is making up a love story that isn't. If this is supposed to convey the devs' message about clerith, then it's really harsh, imho. But I still think cleriths will get more scenes to come. It's in the OG, it will be there in Remake too.