I think the reason Peter's against uncovered vats with catwalks above is a combination of two factors. The first is that people will die accidentally outside during your day to day operations, which is the reason why uncovered vats of hazardous chemicals are a bad idea eye are el, and the second reason is just a restatement of rule 76 - the trope is that if the villain gets in a showdown with the hero near a ledge they could fall off of to their death, the villain takes the tumble.
But you're in a Pathfinder game, and in Pathfinder, combats are resolved based on dice rolls and smart tactics, so this isn't as relevant to you. In fact, including more walkways and bubbling vats of hazardous chemicals is plausibly just a good call, even if you're not doing anything with the chemicals? My team is incredibly practiced at killing all kinds of people and monsters in featureless rooms or open spaces - it's pretty much routine - but mixing things up means we have to think on our feet.
Or we might feel drawn to do foolish things just because it's fun to interact with the terrain, even if it'd be smarter to stick to the tried and true!