I've gone back and forth between manuals and automatics quite a bit. I've found that just where the pedals happen to be in each car impacts the habits. The GT3's pedals are in a relatively narrow arrangement, further to the right than many other manuals. As a result, the clutch in the GT3 is around where the far left part of the Cayenne's brake pedal sits. When I would switch from manual Camry to automatic Sable, my foot was over empty space. When I would switch from manual Miata to automatic Camry, my left foot would just graze the brake pedal, not enough to depress it, but enough to annoy my foot.
Actually, the third gen MX-5 trained me to have my right foot just a bit to the left of the GT3's brake pedal when trying to stop. It caused some... interesting... brake uses from time to time.