I would think that this would be true as you are learning, but once you have been performing the two-foot motion for several thousand miles I would think the action would be so ingrained in your muscle-memory as to remove entirely that cognitive decision. At some point you stop thinking about which foot and just automatically know brake=left foot.
As a lifelong manual card driver with a left-foot clutch, it takes about, oh, ten seconds of sitting in a go-kart with left foot brake and right foot accelerator to get used to it and adapt. There seems to be no real difficulty in switching which leg does what.
