The first part of MN 1 is about how an ordinary person relates the sense of self to a variety of phenomena. It is clear from this description how sticky this sense of self is, in that it will always find something to identify with, even a misconceived version of Nibbāna! This is one reason we have to tread so carefully with how we understand Nibbāna, because most of the time the sense of self will hijack our understanding and lead us astray. And as you rightly point out, no amount of intellectual understanding can eradicate such a deep-seated “notions of self”. Only insight can do this.
When it comes to SN 22.89 and Ven. Khemaka, the situation is a little different. Here Khemaka is already at least a stream-enterer. A stream-enterer has right view and so they would not “see” a self in relation to any of the categories described in MN 1. So, for instance, if you ask a stream-enterer about the existence of such a self, they would deny it. However, their right view does not yet fully inform all aspect of their mental life, and so they may still misperceive a self. The noble person who is not yet an arahant is in fact training to overcome this kind of misperception. In regard to this, MN 1 says the following:
Bhikkhus, a bhikkhu who is in higher training, whose mind has not yet reached the goal, and who is still aspiring to the supreme security from bondage, directly knows earth as earth. Having directly known earth as earth, he should not conceive himself as earth, he should not conceive himself in earth, he should not conceive himself apart from earth, he should not conceive earth to be ‘mine,’ he should not delight in earth.
This is what Khemaka is doing. He has right view, but he training to eliminate all misperception.
Is this what you were asking?