TFM does not say that we control all aspects of the mind. That is obviously untrue. We have no control of our dreams for example.
What I think it's saying is that we can decide the reasons for the sake of which we do an action. For example, I am abstinent now because I thought about it and decided it was something I wanted to do in order to have a healthier and happier life. So I took some action, I did something which was to give up drinking, in order to bring about some effect which I thought would be good.
That seems to me a very natural way of thinking and I believe we think something like this in all other areas of our lives and so it is a very reasonable "generalised assumption" to make.
If we can't think in some way like this it would mean that we have no control of our minds at all, that is, no free will. This may be true but would also be a generalised assumption - a much less plausible one IMO but let's not go there!