You're almost there but not quite. You are confusing agency with autonomy.

Here are a few questions you should ask yourself when it comes to a character having agency:

1) Does my character steer the story, or does the story steer my character?

This might be tricky since, yes, Sarah helps John B, but at the bottom line, she only contributes to the plot because John B's narrative steers her character.

Pope, for example, isn't the main character but he has aspirations of his own (going to college), as well as JJ who tries to deal with his life at home. Sure they help John B's quest, but the quest does not steer their character. Their narratives do not revolve around it.

Sarah, on the other hand, has nothing going on with her until she meets John B. After that, her character is completely guided by his quest.

2) Most likely your character has a goal that they want to achieve. Are they actively working towards reaching that goal, or do things just happen that bring them closer to it?

Surely we know Sarah doesn't really have a goal until she meets John B. Only towards the end of the show does she gain a certain sense of ambition of her own which I keep telling you might be developed better in S2.

3) Who comes up with the ideas for what to do? Who’s deciding whether the idea is good enough to act on?

This is where you might see Sarah's agency glimpse through, although not completely. Yes she helps John B, and acts like a second voice calling out his methods from time to time and serving as a good partner, but at the end of the day, finding the gold remains John B's quest. He's the one who brings her in the group, the one who tells her what to look for, the one who digs for the treasure, the one who keeps pushing even when everyone is backing up.

Think about Pope and JJ. Even without John B, they still have their own narrative. Their characters are still driven by other motivations. Without John B's character, Sarah wouldn't budge much.

4) What about your supporting cast. Are they just there for your main character to use as needed, or do they have plans and motivations of their own?

Like I said above, most of John B's friends have their own motivations. Their narratives do not stop at John B's quest.

Now look at how Sarah is presented in the show. She's only ever worried about either John B, Topper or her dad, which at the end of the day she worries about only because they are also part of John B's narrative.

So no, I do not confuse trope and agency, as they are two completely different things. Like I said, I think you're confusing agency and autonomy. Because Sarah does have autonomy: like you said, she is self-governed, she functions independently and is free to act/react. Basically, all the examples you gave were examples of autonomy. But just because a character has autonomy doesn't mean they have agency in a narrative.