Are these worth shifting based on matchups? Meaning, if I am starting a series against a noodle-armed catcher, should I shift toward a more aggressive base-stealing setting? Or if I left the aggressiveness at average, would my players naturally try more, smarter steals against him anyway than if he had a great arm? Same question for opponent outfielder arm strength and baserunning aggressiveness.

You can during the regular season if you have time. I tend to focus on these and dissect during the playoffs.

I definitely have the time. I'm really asking whether it's effective.

It can definitely make a difference.

I find it does. Of course, I like to have a lot of fast, good baserunners on my team. So that helps.

I do it. Not sure how large the effect is.

I think it is definitely worth doing if time permits.
It may have only a small impact on the super stud base stealer (cause they're going to steal at a 90+ % clip anyway), but will have a larger impact on the guys who are only moderately good base stealers.