1) Focus point was not on the same spot.
2) Spot meter is based on the focus point, so it metered differently since you were on a different focus point which was over something else.
Not a good test as it allowed you to make differences which are user error in this case.
Shoot in manual mode and set the values yourself, don't let the camera do anything you're not telling it to (so they both produce the same exposure, same settings, so they're not different). Meter it yourself. Shoot in One Shot focus drive. Do this from a tripod, tightly set. Make sure there is PLENTY of light, and not just dim indoor light. Shoot wide open (F1.8). Set the focus point to be the center point only. Your subject matter needs to be something with lots of contrast (print a focus board on white paper for example). When you go to focus, rotate your manual focus so its out of focus so that the AF system has to find focus, both in phase detect (your viewfinder) and contrast detect (Live View) to see the difference. Use a remote shutter release, not your finger to trip the shutter as you're touching the camera and moving it (unless you have butterfly touch, maybe you do).
Very best,