Quads are a two-joint muscle group. They flex the hip and extend the knee. There are other critters who can subtitute or compensate.

Downward toes sounds like a substitution of ankle plantarflexion for part of what should be knee extension. (just another way to push the pedal. your body doesn't care what joints or muscles it uses, as long as it gets the pedal to go around)

Pedalling with one foot is a cool way to work the muscles. (and it strengthens those all important hamstrings in the back of your leg!)

Be sure to keep doing both the open chain (like standing hamstring curls) and closed chain (like hamstring bridges) exercises your PT gave you. Hammies are your friends!