It's just the check boxes that matter. Using the percentage can be a good shortcut if you have a different threshold you'd like, I feel like some people gravitate closer to something like 90%, but at the end of the day the boxes are what sets the defensive matchups. Anytime you leave the Game Plan page and come back the number will reset to 95% but the check boxes will stay at whatever you set, as long as you remembered to click Save Defensive Matchups.
As for your second question - it should be very rare, but the sim can also be very random so it can happen from time to time. It would most likely only happen if you had a player get into foul trouble, or it was during garbage time - once the benches clear, the sim seems to throw much of its logic out the window.