Can someone who has had tmj arthroscopy surgery feel misaligned in his teeth afterwards?

Yes: I assume you're referring to arthoscopic surgery of the tmj. For a simple arthrocentesis, no change in the bite would be expected. However, a surgery that alters the articular surfaces of the mandibular condyle, glenoid fossa, or joint disc would effectively alter the angle at which the teeth come together, and could necessitate adjustment of your tooth contours to refine your bite (occlusion).

Yes: A slight amount of fluid may be present in the joint and cause the bite to feel off. This usually subsides after a week or so. Teeth should not really shift after arthroscopic surgery.

Bite seats the joint: The joint is fully seated when you bite your teeth together. If the bite is off the joint position will be compromise. If you feel your bite is off it probably is and you need to find the best relationship for your jaw and jaw joint and then maintain a stable position by completing treatment to a stable relationship.

Yes: Yes, especially early when there is still swelling within the joint. Should settle down. Ask your TMJ surgeon.