It's not entirely clear why Walt has a completely different attitude about Walter Jr's driving style in the episode Half Measures, in which he basically says "as long it gets you from point A to point B" it's fine. Is he being more understanding of his son's disability or he just doesn't care as much anymore? Is this in some sense a "half measure" as well?
Remember that in season 2 episode 4 "Down"
Walt tells his son that he cannot use both feet to drive
You can't use one foot on each pedal
Then in the episode you mention (3-12 "Half-measures"), when Walt notices that Jr is still using both feet, the son tells his father
I looked it up. New Mexico says all I need is a note from a doctor
to what Walt responds "Well, as long as it gets you safely from point A to point B..." and then congratulates him
Walt understands that his son's disability doesn't allow him to drive like everyone else, and tends to acknowledge the driving particularity.