Is there a way to change variables through if statements in a way that they will change in different ways depending on what alternate text the player gets
The Score Changes get applied before the chapter is sent out to the user. If you want to change variables, you have to do that at this point. Currently, you could create two (or more) chapter options which are accessible depending on the current Score. That way, you can change a variable depending on the Score. (This only works if you have only one or two variables with not many options.) The next version might add a more convenient way of doing that, though I suppose that the variable changes will still happen at the beginning of the chapter.