In the interrogation scene with the Darpa Chief is the only time you see Mantis, Liquid, and Ocelot together. In MGS4, Mantis is helping Liquid Ocelot with controlling the B&B corps. (You can see him in act 1 as an easter egg) These might be where kojima got the idea to retcon it in, much like with the venom snake into mg1 retcon. It's something that wasn't hinted at before but fits in nicely anyways.
I wonder if Mantis could read Ocelots mind so thoroughly that he would know it wasn't really Liquid?