The Brexit/Alberta separatism analogy isn't about comparing a state leaving an economic union to a province leaving a nation. Alberta separatism, if successful, would have a vastly more significant impact on its people than Brexit.
The analogy is pointing out how political movements that initially demonstrate limited support can take on a life of their own, ultimately leading to outcomes that those who voted in favour didn't actually intend. Especially when fed by arguments that are divisive, opportunistic, emotional, nationalistic, and misleading.
That's the prospect being raised here; that a lot of Albertans who vote for "sticking it to Ottawa" or "generating leverage" are going to wind up with a basket of negative political and economic consequences that they didn't initially think possible.