Excellent suggestion, thank you! And with a bit of looking, I actually found an essay by someone who uses Zendo to teach the scientific method. I incorporated your suggestion, as well as a brief excerpt from his essay:

Zendo, also known as ‘Science, the game’, involves one player picking rules and creating structures that follow that rule. The other players try to discover the rule by building their own structures and asking whether those structures follow the rule. See Wikipedia for the exact rules.

Traditionally, the names of these roles are ‘Master’ and ‘Students’, but one may also call them ‘Nature’ and ‘Scientists’ - as the players can be thought of as researchers conducting experiments in an attempt to uncover the hidden laws of nature. One author, Nick Bentley, writes that he uses Zendo for teaching the scientific method, and names four issues which relate to the scientific method and also pop up in the game (the whole essay is recommended reading):

Here's the great thing: issues that pop up in real science also emerge in the game. Here are four:

1. Ambiguous Hypotheses - Sometimes, a Scientist will state an unclear hypothesis. In this case, the universe must ask for clarification to construct a counterexample. This is one of the central problems of real science too: how to construct testable hypotheses? Zendo's a forum in which to practice the kind of precise language needed to do so. Awesome.
2. Superstitions based on spurious correlations - Sometimes, thanks to the Scientists' experimental choices, a pattern of white and black stones builds up on the table which all conform to an incorrect hypothesis about the law of nature. This is how real Scientists get stuck too. And just like in real science, you get unstuck by finding an experimental counterexample to the incorrect hypothesis, at which point the Scientists undergo a "Paradigm Shift". Paradigm Shifts also happen when new investigators without the usual biases (who can interpret experimental results in a new way) enter the field. For this reason it's said that science proceeds by retirements (the older biased Scientists retire and make way for new and differently-biased ones). In Zendo, the same thing happens when someone who's not even playing walks by the table, glances at the experiments, and points out a hypothesis that the players missed due to group-think. It makes clear the value of fresh perspective and independent thinking.
3. The value of simple, systematic experimentation - In Zendo, it helps if Scientists do experiments in series, where each experiment differs only slightly from the last. This allows Scientists to quickly pinpoint the variables that matter to the experimental outcome. Scientists also learn to minimize the number of variables in each experiment, to minimize the chance for spurious correlations as described in point 2 above. These are essential practices for real Scientists.
4. The value of Occam's Razor - Scientists quickly learn how to make their hypotheses as simple as possible, because then it's easy to interpret the counterexamples that disprove them. The more parts a hypothesis has, the harder it is to infer from a counterexample what part is wrong.

These are the fundamentals of the scientific method, and Zendo presents them as no real-life lab exercise ever could, because it presents them free of the distracting technical details of real-life experiments. There's no faster or clearer way to learn them.

Thus, becoming better at Zendo involves becoming better at the basic skills that are used for forming hypotheses about reality. In particular, it teaches one to be wary of confirmation bias, as players quickly realize that even hypotheses which fit all the existing data can easily be wrong. It is also useful in becoming more aware of the illusion of transparency, as it is common for the Nature player to develop a rule which seems easy and obvious to them, but which turns out to be very hard for the players to guess.

One early surprising result of Zendo is that what you think is an "easy" and "obvious" rule is probably illusion of transparency in action.