You choose your faction, then determine strategies, then build your crew.
What this means, is that you know your opponent will be neverborn with treasure hunt. And they know you will be arcanist with assassinate.
They can then choose to build any legal crew with a neverborn master and the models they have (or proxy). Most players locally have a limited selection, such as myself, so it tends to be one master, with a selection of various minions, but if they have multiple masters from the same faction they are free to choose which one to use based upon your faction and your strategy.
This can introduce some balance issues when a new player with a small selection plays somebody with a much larger force, in that one person can tailor to the game much better than the other. If this is an issue, you can always agree to predetermine lists, or restrict the number of models available to choose from, or some such.