Player Agency means simply that players have agency for their actions -- i.e., their actions can change the town, nation, or even world. If I'm running a module, and it doesn't matter what the player's do, after Scene 1 they will go to Scene 2, then that's a lack of player agency. It doesn't matter if it's a well-written sequence of scenes, if the players' actions are meaningless in the grand scheme of things, then they have no agency. You might as well be writing or reading a short story. I've run modules where one character absolutely will die, it's written in, and the module has no alternatives for if they survive. I've written scenarios where, once the BBEG is killed, the rest of the dungeon becomes unreachable and the PCs have to flee for their lives.
When someone tells me, "I hate Player Agency," it tells me they already know how they want a scenario to end. They've already written the finale, and if they let the PCs change things, then it won't finish neatly and elegantly like they wanted. Why bother playing at all, then? Play to find out what happens!