There is kind of a contradiction between two rules 16.3 and 17.1, in that they both claim they are "not superseded by any other rule".
I think the interpretation is that if a foul that occurs according to 17.1 is deemed to have not affected play according to 16.3, then play stands(?). So both of the rules are able to be applied simultaneously, without superseding the other. This also seems to make the most sense to me.
However, I can see how the wording could potentially cause confusion, e.g. if a player argues that they were fouled according to 17.1 and no rule can "overturn" this foul (i.e. their interpretation of the supersede wording). Perhaps clarifying this would be a useful addition to the annotations, or a mention in rule 17.1 that 16.3 may still be applied (assuming my interpretation is correct).
17.1 says it is to be treated as the most relevant foul from Section 17, which could include treating it as an Indirect Foul (which is another way of saying that the foul did not affect the outcome) so therefore any play would stand.
Also 16.3 says, yes it was a foul, but the result will stand.