From my experience issue and counterpoint comes out by itself when your write and do revisions.
Before I start with the first draft its more guessing what it might be. There is a lot of fixed mind working in the first place ("ah, this is morality, its for sure, and this is ..").
But often its a surprise what is it and what I am writing about. To accept the unknown and start writing works much better for me nowadays.
In the beginning with Dramatica I also tried forcing it - because I like(d) the idea having something to say with my story. But the result was stilted with no blood.
Today I revise my first, second, third .. guess until the issue and counterpoint makes the most sense to me ("uh, I never thought about it could be interdiction, but it makes totally sense, no I understand why the other is always pushing.."). This is especially true for the throughlines.